Alright, here goes...
So, people have alleged that the US government (among others) keeps a wide network of underground bases, and all sorts of theories have been put forth about why they would need so many, far beyond what you'd expect for simple continuity-of-government/bunker functionality. Alien treaties, human experimentation, cloning labs, etc...in this case, I'm just suggesting that one of these purposes is to shield quantum computers from cosmic rays and other types of particles that can go through anything but a large amount of compacted matter, because of how rarely they interact. Unfortunately, for a quantum computer, that rare interaction can cause the decoherence of a stored qubit state, or in simpler terms, scramble up the information of that quantum bit by interacting with it and, in so doing, rendering the information unreliable. All that extra noise chews into your processing power, because you need to use up some juice on redundancies and error correction tasks.
Now, you've probably heard people say that military tech is often decades ahead of what's commercially available...and quantum computers have tons of defense applications. So, if quantum computers are just about to become a commercial product now, how long has government had access to this tech? (I could ask the same question about net gain fusion...you should check out those recent US Navy patents - which were filed just a few months before public scientists were expected to achieve it.) If this were the case, it could certainly account for some of the facilities and the need for them to be underground, though likely not, as polymoog pointed out, all of them. I still think secrecy is the prime motivation for placing most of these facilities underground.