PTW AI doesn't put a huge emphasis on navies and is probably just running with the vanilla navy AI. I think the learning algorithm Soren put into vanilla Civ will kick in with 'unknown' conditions and you'll see the odd AI with a large fleet.
The navy AI got a bump in C3C and you'll see a much more diverse use of ships by the AI. I've run numerous debug games on this, usually on STD - continents maps, and the strong AIs can field some pretty mean stuff. Carrier fleets, and stacks of invading fleets. one AI had 70 odd destroyers on a standard map!
Usually you're more than likely to see the usual 1 transport escorted by 2 escorts (the best ship AI has) against most AI opponents. But I generally play on standard/continents maps where navies do come into play and the AI does put more emphsis on ship building as part of its exploration/colonization process so I may be seeing more ships than the Pangaea players.
That said, like the airforce, navies are usually the first thing to go when an AI economy is buckling under a sustained war as they will usually be unable to replace ships fast enough and what you'll see is at the war's outset, you'll face a formidable AI fleet that dwindles overtime, (assuming you're killing the ships) and they usually don't recover to their pre-war levels unless you sign a peace with them. As with everything, there are exceptions. AI's can sometimes set their coastal cities to build ships all at once, and in the middle of a war, there can be waves of new ships coming out every 5-10 turns.