Something important to note is that Steam has the Megaton edition whereas this is just the Atomic edition. What that means is that while this is technically the full game, Steam's release is the full game with extras, namely the official expansions "Duke it Out in DC", "Life's a Beach", and "Nuclear Winter". The GOG release here does not have these episodes, "Nuclear Winter" is just ok but the other two are definitely not worth missing. Plus the access to Steam Workshop makes installing mods even easier than before. I highly recommend getting the Steam version of Duke Nukem 3D if you want the full experience. However, other than those missing episodes GOG's Duke Nukem is still a flawless port of one of the best FPS games of all time with mod compatibility intact. One thing Atomic has over Megaton is that it is cheaper. Either way though, you are getting one of the best FPS games of all time so you can't lose.
