It's actually possible to file a patent along with a secrecy order. This is done to protect the government in case someone else ever tries to patent the same idea at a later date. And before someone freaks out, this is not new. It was imposed during WW I, WW II, and then codified in the Invention Secrecy Act of 1952.
In particular, patent GB630726 by Leo Szilard, Producing neutrons, covering nuclear chain reaction, was one such secret patent. I think it probably was a good idea to keep that secret.
This is why you don't patent stuff that's supposed to be secret, regardless of what other people think