Does the crew of a ship get subtracted from the planetary population with the shipyard?
They get subtracted from the Crewman and Junior Officers (CJO) total shown on the Personnel tab of the economics window. These are produced by neval acadamies. If you don't have enough CJO, the ship will start with an inexperienced crew with zero grade points (and thesefore a -10% grade bonus). If you don't want to use up CJO for certain classes, such as freighters, you can flag these to use conscript crews on the Ship Class window.
Steve