I'm not sure the point is actually to keep it secret, but (as with all government "services") to cover the arse.

Also, if you were an employee in a company in this situation, and you'd been told that the security of the nation depended on your silence, and more to the point, you'd be locked up and your career ruined if you went public, what would you do? Whistleblowers are pretty rare, because the consequences of doing that are huge.