“a giant fleet of PT boats would struggle because a) they don’t have much range and b) they aren’t very seaworthy.”
I’ve never played this game, but I would also think that such a flotilla also would be very vulnerable to being taken out with just a few large weapons (e.g., fuel-air explosives, as one example http://www.youtube.com/watch?v=j9xCgNdZPKk). So yes, the sheer number might preclude taking them out with individual rounds of artillery or whatever, but their small size and inferior seaworthiness would correspondingly elevate their vulnerability to other types of attacks.
There’s also the morale factor to consider. Even though the game shows a giant PT boat fleet defeats any enemy, it will always suffer heavy casualties as it moves in. That’s ok from a command viewpoint but the jolly jack tars in the lead boats might disagree with the rationale :)