Actually, yes you do block all cell phones and transmissions in these
facilities.
Are you talking about a SCIF -- Secure Compartmented Information Facility? The sort of place where they basically Tempest-shield the entire building?
Yes, those are huge Faraday cages, and they do completely block all signals going in and coming out. However, while there are SCIFs inside the Pentagon (including the National Military Command Center, or NMCC), the entire Pentagon itself is not a SCIF.
Classified environments are very different
and have an entirely different set of requirements.
Indeed. The scariest thing I saw inside the NMCC was their complete lack of regard for internal security. They assumed that if you made it past the guards, you obviously had clearance, so they didn't bother locking up classified material when they were done with it (just at the end of the day), they didn't bother covering classified material while it was on their desk but they weren't using it precisely at that moment, etc....
It's pretty damned entertaining to take your parents through the NMCC on a private tour, and watch everyone scramble like hell when they figure out that these two middle-aged tourists don't have a lick of clearance. 
Oh, and yes -- I did take them to see the Crisis Action Center, including the DEFCON board. However, the DEFCON status for the Unified & Specified Commands had been blanked, because I told the officer on duty that I wanted to show them the room from the viewing balcony above.