I'm worried about the pass through shots and the powder magazine.
As already stated, cannons were in the gun ports and they took up most of the room there so it'd be very hard to actually miss anything, and then if you did miss something on the first side you were highly likely to hit something either on the inside or you'd hit the other side of the ship after going through the first gun port. The chance of a cannon ball just going clean through are very very minimal.
Also like others have said a million times, the magazines were always below the water and behind the strongest armor for the exact reason of not blowing up. Even if there was a fire on board the crew very quickly doused it out.
I also like the current aiming system, but it will be interesting to see what you come up with. Other than that I love the new damage model.
Keep it up guys