There is a distinction between "above board" and "below board" crew. The above board crew are the ones manning the sails, helm, cannons, etc. If you cripple those crew you turn their ship into a lame duck. Grapeshot targets the above board crew.
The below board crew is where the soldiers are. The number of below board crew is shown as a number under the enemy captain's portrait. You can injure these crew members, sometimes, when firing at the enemy ship's hull with normal cannonballs.
Hope that helps.
