Yeah, there are different compartments modelled on the ships and it does matter where you hit them. I know that flooding and fire damage also can affect the way ships sink. There are mods that refine it and make it more realistic. One to check out is Arclight's BARF mod.
As to where to hit ships, it depends on the ship and I've just been learning through trial and error. I try to aim for the keel or the engine compartments. I know on ships carrying munitions if you hit the cargo stores they'll go up in a Michael Bay-splosion. Hope this helps.