Don’t Shoggoths dissolve when you kill them? Also, that room is going to be radioactive as fuck, I wouldn’t go back in there without a rad suit.
A trap hallway MIGHT work on one shoggoth, maybe. Even if you had a hall solid with landmines it might not be enough. Even if they didn’t set each other off, those damn things can take a beating, and they regenerate like Deadpool constantly. A whole horde of them is going to take trivial casualties, then run amok through the rest of the lab.
God help you if they reach the surface.