No cellphones are allowed in top secret military locations in the US, because all can be remotely signalled to start recording audio. We know they'll turn a phone into a bug if they need to, so it's foolish to assume they wouldn't be able to get the real PIN.
Do you have any evidence that indicates that this is the reason?
A much more likely explanation for the policy involves abuse by the user, either intentionally or unintentionally. Cameras and USB sticks are similarly restricted.
