Humor me, why is this unlikely? Why is it not possible that (whatever three letter agency) grabbed a few engineers, told them to do X without talking to anyone else, at the risk of them and their families getting disappeared to a black site?
Besides, in security controlled jobs it's perfectly normal to not be allowed to disclose what you're working on even to your direct superior. This idea that Tim Cook / Apple PR must know everything that's going on at Apple is kinda ridiculous.