RealGM

This is a pretty dumb question but I'll admit I don't know for sure if Player A plays in 81 games, is the game he missed treated as 48 minutes without him on the court or is it treated as if his team only played 81 games that year.

Well, he didn't play, thus it is treated like that. ;) The missed game are at least 48 minutes the team played without said player on the court.