I have +500 games on steam and I have never had any problems. To be honest having a game up-to-date automatically is a big plus for me.
I also almost always mod my games and except for Silent Hunter 5 I've never had any problems. Yeah, sometimes it happens that a steam game requires a different procedure to mod but only in case of Silent Hunter 5 steam has shown me the middle finger.
I suppose it's because the vanilla SH5 is in the absolutely worst conditions.