I wouldn't worry too much about modding. Remember, one of the most modded games in history (Half Life 2) is on Steam.
A few games had issues with modding, but that's because there were multiple versions of the game released (retail, Steam, D2D) that were all patched differently.
Most Steam games are patched the same as retail now, so those issues are mostly gone. With a Steamworks game, they can ensure that everyone has the same base version of the game so it might make modding easier.