I know virtually nothing about military weapons. But I do know about blasting rock and have done my fair share of it when I was young. It is hard to understand how those bunker buster bombs could damage a deep underground facility. Quite a few times I have been a couple of hundred metres to the side from a blast a couple of tonnes of explosive at a depth of around 1000 metres below the surface. I put my fingers in my ears, and stood in a side tunnel, but was never in danger of being blown up. Nothing was damaged in the mine, other than the rock being broken where it was intended. This happens all the time in large mines with large stope blasts.
So if the bombs did not penetrate the facility, the shock wave probably didn't destabilise the tunnels and galleries very much. If they had centrifuges or delicate machinery, then it could certainly have been wrecked. My point is that the tunnels and galleries can probably very easily be reinstated and are not actually destroyed.