I think you are describing a situation that will never happen. We have bombs now that can penetrate underground bunkers, yet we still insist on building underground bunkers. I have noticed that human beings, when threatened or under attack, like to cocoon themselves. There is something about having a thick set of walls between you and the outside world. I don't think that will ever change.
I think that electromagnetic shields would be incorporated into a secured facility. These shields would either protect the whole facility, or would section off parts of the facility to isolate and quarantine intruders.
I was doing some research. The Pentagon has two levels that are underground. In affiliation with the Pentagon, there is the Raven Rock Mountain Complex. (http://en.wikipedia.org/wiki/Raven_R...untain_Complex
) This facility is described as having five buildings, each three stories tall, computer filled caverns, and a water reservoir. I think the key points in secured facilities is that they are not visible to the public, that they have communication links with the outside world, and that information about them is classified.
If I was a high ranking Starfleet officer, and I was told that I would be meeting in a conference room in a skyscraper for an emergency conference, I would be immediately suspicious of the circumstances.
I think showing this facility in the movie would have been a plus. I think it would make the Federation and Starfleet seem more real, that somehow these entities have a connection to our world. I was hearing one review where the reviewer felt after watching the two reboot films that the nature of the Federation, and Starfleet, was ambiguous. I feel that showing this facility might have given us some insight into both. When I think of people meeting in a conference room in a skyscraper, i think of board members belonging to a corporation.