Do I get less scrap if I "soften up" an enemy ship before I board and finish off the crew?
According to this wiki page (and to this Arqade page, where a rather similar question is answered), the default reward system does not take the "health" of the enemy ship into account when the ship survives. It is only a matter of probability between the possible rewards triggered by the "killing the crew" victory.
According to the Developer, it does not.
Update: It was a comment made by the Developer on the now-defunct Penny Arcade Report website back in the day. Apologies for not linking to the source originally.