Unfortunately the answer to that is a resounding. No.
Steam's version, as of this time, is incompatible with gamesys mods and there's questions on whether multi-player will work right or not. That does not mean mods cannot work. That means mods that affect how the game plays (ADaoB and an upcoming mod that provides more in depth and thorough fixes) WILL NOT WORK out of the box. Even the patcher tool itself will not work, and as of this time Kolya has said he will not make an extra effort to add stea mfixes on top of the fixes for the gog release.
A post has been made detailing how to fix this. User Kolya from SystemShock.org, maker of the patch tool that NightDive used (then failed to give credit for using.) My last post related to SS2 went at length, providing links and quotes about NightDive's claiming credit for community efforts in the GoG release. Steam has gone to the trouble of stating that they simply put up the version of the game that NightDive gave them. User Kolya, the guy that provided the community patcher tools, directly sent them a prepatched and known good copy of the game files where all they'd have to do is send the image to Steam and so far that has not been done.
I am conflicted feeling on the issue. On the one hand if somehow the multiplayer problems that've plagued System Shock 2 were somehow squished and steam's community features could be leveraged I'd call this a good release. As is with a half-broken install and NightDive still going with the song and dance that 'they' did all the heavy lifting. Yes I'm going to trot out a Rock Paper Shotgun quote.
There are some user-made mods out there which do phenomenal work on the game’s stability, but none of them were quite perfect, so we took the game to our expert techninjas to analyse and swat the remaining bugs.
Mister Kick. Stop claiming credit for doing more than what you've done. Granted what you've done is nothing short of phenomenal since it makes a game that's been highly praised for the past thirteen years legal to buy. However please give credit where it's due. Work with the community. Invite them in since they're the ones that've done the heavy lifting and given you a fanbase to make this game worth acquiring the distribution rights for.
Be honest with everyone. That's all I'm asking.