What's most effective depends on the gun you're firing with! If you are working with a Goldfish and a Carronade - shoot the balloon, and only the balloon. It'll first keep the enemy ship on the ground, and secondly the damage gets transfered to the hull, like you said. If you have your gunner start shooting the hull, then the enemy ship only gets time to rebuild their balloon and the whole game starts again.
By shooting at an empty part of the ship that doesn't have anything attached, you are most likely hitting the hull already, it should have the greatest hitbox of all (except the balloon maybe), and out of my mind I'd say that everything that isn't a gun, engine or the balloon is automatically the hull.
And yes, as mentioned above - shooting at a already destroyed gun, engine or the destroyed balloon will transfer the damage to the hull. Of course damage reductions still apply! So, if you are shooting with your Scylla Double Barrel Mortar at a destroyed balloon, it'll actually do less damage than if you were shooting straight at the hull.