It may depend on map type. I'm playing mostly on hemispheres/Immortal, and have got hit by a very substantial enemy navy in the late phase of the game on several occasions. On no less than three occasions the best AI has slung everything it has at me immediately that I launch a spaceship and, since I don't like sharing a continent, they've all been naval invasions. Nukes I agree are rarely that relevant - if there are other AI's at a tech level to build these, nukes are so easy to ban with the UN that they're never really an issue. There's at least one random event that lets you ban them without worrying about the UN as well. I've certainly never had to worry about a nuclear strike.
The AI is very fond though of sending literally hundreds of guided missles into your terrain improvements from subs and cruisers, so it is worth keeping a few scouts out - but only attack subs, and I usually find it easier to watch the ports of my enemies (assisted by espionage) than to stretch forces across my whole coastline. The cost of a defensive net as you suggest in your article is horrendous, and the classic AI naval stack (30+ missle cruisers, 40+ destroyers, 30 odd subs with missles and assorted carriers and transports) will punch through it like tissue paper.
The trick is to look for enemy stacks while you're at peace and they're in port. Then when war comes you've got a good idea of the direction they'll come from, and how long you've got to intercept. You have a couple of stacks positioned so they can reach any part of your coastline within a turn or two, and have a handful of attack subs as an early warning system out at sea. I think it's your focus on stealth destroyers which is the main problem. While I agree modern naval warfare is now important, I've yet to see stealth destroyers be relevant, for the simple reason that Stealth is invariably the last tech to be researched. Also, it isn't a problem if they do get through to your coastline - they can't carry missles or troops and they can't escort transports because of their broken behaviour. At worst I lose some fishing boats, and I assume that will happen anyway. It's a SoD you've got to worry about and a thin layer of Stealth destroyers isn't necessary to spot it, and won't even scratch it.
That's an excellent point, and I think navy is probably tops in water-heavy maps or instances of full-scale intercontinental invasion. Nevertheless my first instinct is the same as Invis's post--if you have that many hammers, you are better off using them proactively rather than in an passive force. Meaning, load up the transports, boys!
