The Jap AI sub is acutally a cloned Type9D2 from the uboat addon by Natilus42. I think he then touched up the conning tower so it more closely resembled a japanese subs conning tower.
I then came in after him, and changed the zone ID assigments of the submarine, which by default are the player damage zones (bow torpedo room, engine room, command room, pumps, etc). I changed the damage zones to that, i think of a large warship. Primarly because the zone definition had a high flotiablity rating, and a nice explosion attached to it. A high flotablity means that it takes a larger chunk of the overall subs boyancy. This (in addition to lowering its HPs from stock) is why it will sink now. The only catch, is i can't redefine the size and shape of the damage zones (well i could, but i have no 3rd party app to see what im changing them to, so its a moot point
), so the zones are shaped how they're shaped. The damage system against subs is anything but perfect. It is however, passable.
Nautilous42 also made a similar mod for an AI monsun boat which appears at the historical dates in logical areas like the java sea, and again i went in after him and reworked the zones in a similar manner to the jap sub.
I have not however, gotten around to "fixing" the damage zone ID assigments to the jap midget sub or the I-400, so they'll still essentually torpedo sponges.
You'll find the jap AI sub and german AI sub in TMO, RSRD, and i *think* RFB (not sure). You won't find them in stock.