This is a highly subjective area. As you know, the game comes with some stock designs, but especially in the mid to later game, they are few and far between. And also, you should remember, they're basic basic basic designs. Personally, i say you should ALWAYS design your own ships (and i don't neccessarily mean from an aesthetic standpoint).
Personally, i update my designs every time i research a new weapon. That way whatever get's built is the newest version. What's the point in building an obsolete ship if you can afford a newer one?
Now as to fleet variety, that completely depends on what you will be up against. Many of the races prefer different weapon types. The Drengin, for example, like missiles most of the time. So if you are designing fleets to take on the drengin, i'd make them with heavy Point Defense. And i would also take a look at what kind of defense they are using; if they're using shields for example, i would load my ships up with missiles or direct fire weapons.
But in a broader, general sense, if i was making a general purpose fleet, to take on anything that might come it's way, i would design several ships devoted to each of the weapons types. I'd have Gunboats, Missile ships, and Beam cruisers for examples. And not knowing what they would come up against, i'd put some of each defensive component type on them. Remember, the more defenses you have, the longer your ship can remain in the fight. And sometimes a ship that's able to hang in there longer can defeat a ship with superior firepower but with less defense.
So in short, i would say designing your own ships is the thin line between victory and defeat. So i say, design away, and often.
