Actually, firing on the uproll was the preferred French (and Spanish) strategy, with the assumption that if you immobilize a ship it is then at your mercy. How well that worked out is illustrated by the battle history between the Royal Navy and their Franco-Spanish adversaries. But you make an excellent point, in that once the ships were at close range, it was in essence a slug fest, where fire was predominantly directed into the enemy ship's hull. That's why rate of fire was so important, something most Royal Navy ships excelled at.
You raised another good point, in that there weren't many men in the rigging during a battle. Ships would reduce to "fighting sail", generally topsails only, once battle had been joined. That meant they didn't need men aloft and could focus the entire crew on fighting the ship. The only people aloft would most likely be snipers, and certainly there wouldn't be officers in the tops. In addition, they would have rigged slings across the deck to protect themselves from falling spars (partially effective) and gruesomely, falling bodies.