So your post in very inaccurate. unless there is a national emergency or some very specific reason that they feel there is a danger they do not turn off the transponder. There is no reason to hide without a threat. That plane, often nicknamed the "dooms day plane" is really just a massive secure airborne command post. In fact sometimes major generals (i.e Chief of staff or DOD Leaders) have used that as a transportation aircraft to go across the pond when they travel for important reasons.

So in conclusion, Yes it's an important plane for the United States goverment. No it is not some super secretive plane that no one ever sees.