After fighting my way through the tunnel after the lobby battle in ‘Questionable Ethics’ I went to open the large blast door at the end of the tunnel and lost ALL my weapons. I reloaded the quicksaves and the game itself several times (my last actual save is waaaaaaay far back). I can spawn weapons for myself with the console and shoot them just fine, but I can’t see them at all.
Same happened to me, loading an old save did the trick, I had to do the big battle of the lobby again though.