Where should I aim my chain shot?

I really love the naval combat, but you're so busy at times that my answer below might be off a bit. This is how I experienced it.

I went for realism and tried to shoot the main mast on the ship with my chain shot. After a while, a mate suggested to shoot the hull. Shooting the hull itself doesn't do more damage, but it gives you an extra chance to get one of those swivel targets that do add a lot to damage. So there is a potential damage increase, but not guaranteed.
The bigger the ship (better armored actually, but there's a correlation), the less damage you do on the hull though. The first big Spanish ship I had to fight (I forget its name) did not take much damage from shooting the hull with the chain shot, but shooting the masts did seem to bring down its turning speed.

Generally speaking, I like to aim for the masts of ships bigger than the jackdaw, and aim for the hull on the smaller gunboats and the likes.