I'm not sure where I read it but I think beam weapons do only half the normal damage against planet. So let's say we have a normal mass driver with the base damage of 6. When shooting a planet, damage gets halved to 3, and if the planet has a radiation shield, the damage is always zero because the shield blocks it. With this math, normal disruptors (40dmg) do zero damage against barrier shields (20 dmg blocked). I can't test those right now, but it fits my experiences.
I'm not sure, but I think you need to use a heavy mount version of any weapon to damage a planet. Also, planets have something like a base of 3-5 natural shielding that is subtracted from the damage figures. This is without any added shields such as radiation or barrier. The shields themselves subtract 5-radiation, 10-flux & 20-barrier. It seems to me that heavy beams don't do the heavy amount of damage against a planet and also, it is their regular mount rating that is used to determine if they are able to do any damage at all. In past games when attacking planets, I've noticed that heavy weapons I've used consistently failed to damage the planet, yet their damage should of registered some effect since it was above the protection rating. But their regular mount damage was less than the amount required to get through the planet's shield protection.
For example in one game I had battleships with Hv graviton beams (4.5-22.5 dmg). When attacking planet with a radiation shield, they did only 0-5 damage which is like... nothing. Btw, graviton beams are quite good because they can even punch through heavy armor. The 'extra structural damage' is nearly equal to the normal damage. So you need to only shoot away one third of the 'heavy' armor, and the ships blow up because structure points dropped to zero.
Do graviton beams destroy structure through hard shields? I've not seen much damage to ships using this weapon. I've gotten better results using mass drivers (w. armor piecing) since they destroy both structure and systems. But hard shields negate the armor piercing special. I tend to use the gravitons against planets or when against ships, to punch a hole in the shields so the ap mass drivers (or later gauss or ion pulse) can fry the internals. All of these earlier beams are not very good against planets, as you mention, they barely surmount the shielding.
The problem with bombs is that to use them you have to move into the point blank range, while the defenders keep shooting at your ships. In the worst case, the planet has a stellar converter shooting a couple of ships which is, umm... bad. Also bombs can only be used against one type of target which wastes space from other weapons.
By the time you get stellar converters, the time for bombs has long passed. It's early to mid game I use bombs. Late game, most of the beam weapons are more than enough to knock out planet defenses. Faced with ground batteries, I try to do as much damage as I can before they get a chance to fire. If I can take them out on the 1st turn, that is ideal. So beams are the 1st choice where practical. But that ability only comes later in the game. I don't usually add bombs to ships other than specialist planet attack ships which are intended to go after the planet defenses at the outset. Early on these ships are armed mostly with bombs and with 1 or 2 anti-missile/fighter beams. Later, I will add torpedoes and a maybe few mid level beams. By the time I get plasma or disruptors, those designs become obsolete, since my regular beam warships are then adequate to see off any planet defenses. The time taken to get bombs to planet is not so great as you would think. It takes 3 turns at most to reach a planet and bomb it. If you have transporters, it only takes 2 turns to reach the planet. Missiles take 2 turns to reach the planet at a minimum. So the time till you start doing damage is almost the same between bombs and missiles. Protecting the ships in their run up to the planet is no real problem. Give them heavy armor or reinforced hull, or both, if you want. Better yet, neutralize the weapons that will target them before they shoot. The bomb ships are only 1 type of several I use early game. While the bomb ships make their runs, the other types take out the other side's ships and orbitals, along with the defensive missile volleys and fighter swarms. If the bomb ships are 1 size smaller than the main attack ships, the AI's heavy beams tend to concentrate on the larger ships. The bomb ships might number 2-4 out of an attack fleet of 2 dozen ships or more. One other advantage of bombs is they are cheap and you can pack a lot more of them than you can missiles. They also don't run out of ammunition during a normal battle like missiles do.
In the early to mid game, I think missile boats are the best way to bust planet defenses, like this:
Missile Battleship
Systems: Battle pods, Fast missile racks, Reinforced hull if armor is not good
All the space filled with 2x ARM FST (maybe ECM, MIRV) missiles
When the battle begins, move forward, unload the salvo on the planet/battlestation, and retreat immediately. You could have one frigate moving towards the map edge in the meantime. If the defenders can't destroy the battleship in one turn and cause a drive explosion, they won't stand a chance! 3 of these with non-mirved pulsons can inflict 2000+ dmg on the planet. You really have to be careful to not destroy every single living thing on the surface.
That's one of the main reasons I stopped relying upon missiles to take down planet defenses. Overkill. It's easy to over do it and wind up with a glowing rock. I like to try and take the planet as intact as possible. That way I don't have to wait 50-100 turns while it builds back up from scratch. When I first started playing the game, I used missiles extensively, and got a lot of glowing rocks, but now I only sparingly use them. Early game I rely more upon interceptors against other ships, as they are harder to kill and do more damage than missiles. Against planets, I prefer using bombs, as I explained above. Later game, I use mostly beams. The time delay of missiles (or torpedoes) I find makes them much less useful against ships than beams, when I do not want to feel the other side's first beam strike. Especially if they are par or higher in tech. I want their ships neutralized before they shoot, not after.
It isn't till mid game I usually build any ships of battleship or larger. They take too long to build and I have too few planets capable of the industry to build them. They take about 20 turns to build at that time. Early game, I usually only have 1 or 2 planets even capable of building cruiser size in a reasonable time frame. Even these can take as long as 10 turns to make. I look at a rough average of 6 turns building time as a reasonable building time for a ship and scale a planet's industrial capacity to the ship size. Also, these high industry planets are usually needed for colony ships, not warships. Most of my planets still don't have orbitals and are limited to destroyer and smaller, of those that can yet build any ships at all. You'd be amazed what a swarm of destroyers armed with a couple of interceptors and 1 or 2 nuclear missiles can do. Just 6 of these took out a space crystal in a current game and they suffered no casualties (I need to mod the monster's armament suites - if I can find out how it's done - they are too easy to destroy). Nice thing about fighter armed ships is you can fire off the fighters on the 1st turn and then retreat the ships out of harms way. If you are defending a planet with an orbital or base, you can retreat them off the battle map entirely, and let their fighters work their magic after they're gone. In the early game when most of my planets are still developing, I find a destroyer is about all they can reasonably build, so I build swarms of destroyers.
Ultimately, what you use, and how how you use it, depends on what you got to use to begin with. If you're not playing a creative race, you may not get half of the weapon tech, and will have to make the best of what little you got.
Just remembered there is one special called sub-space teleporter you can get late game that makes bombs useful again at that stage. Since it teleports the ship up to 20 squares, a ship armed with bombs and teleporters can start damaging a planet the very first turn. Since the damage to ship space ratio of the last bombs is so obscene late game, 1 ship can practically take out all the planet's defensive batteries. I'd forgotten how late game I used cruisers armed with these sub-space teleporters, transporters, a battery of anti-personnel beams and a couple enveloping heavy plasma to wipe shields, to take down late game titans and doom stars in the 1st turn before these had a chance to fire anything. If I had these cruisers in numbers equal to the number of opposing capital ships, the latter never even got a change to fire. If not, I just captured the most powerful ones and used the rest of my fleet to annihilate the rest.
I have only been playing for a week so I am pretty nooby and have no idea how to deal with Rad/Flux Shields. Beam weapons and missiles don't do much of anything to them and I am hesitant to try adding bombs because I would have to refit a fleet of ships or make a new fleet. Any help would be appreciated 
At that time we each had 25~30% of the Galaxy each pretty bloody seeing how it was an 8 race game. Then as time wore on and we stared at each other wondering who was going to make the first move then Sakkra invaded the Silicoids. I jumped in after they went at it for a few turns seeing which side was winning. So I attack Sakkra who was completely destroying the Silicoids thinking that there fleet was on the other side of the galaxy and it would be easy pickings. I was wrong 
I ran into a wall hard and lost several ships so I changed my strategy to blitz raids. I would attack a system destroy the battlestation and as many ships as I could and retreat until I destroyed every one I could reach. So where I stand now is the Silicoids are pretty much dead 2 systems on my boarder and I have to fight the main Sakkra fleet which was busy while I raided the "bottleneck". Most of my fleets have Graviton Beams and Mirved Merculite Missles and need to be refitted but thats not going to happen 
They need to hold the border and help me try to claim the ruins of the Silicoid Empire from the Sakkra. If I could make progress on the shields I could invade there core systems and win the war/game but I don't have the numbers for that. I have 4 titans, 5 battleships, 11 cruisers and a 9 destroyers to defend my empire on a huge map. Well I am ranting better go 
