Originally Posted by
Burley
(Didn't read everybody's responses. Sorry if there's overlap.)
Lets say you use "Chain Shot" (two balls connected by a chain). It'll do damage to the ship, specifically to the mast on a crit, and perhaps to crew members nearby. If you do crit and hit the mast, the ship is considered immobilized until fixed.
Consider facing and size, as well. If you are using cannons, wailing onto the back of the ship will destroy the rudder. Attacking the side of the ship (broadside), will do the most structural damage, but also leaves you open to take a lot of damage. Attacking the front doesn't do much damage, and leaves you open for ramming, which can just tear you open.