If you've been under the impression that FIDO is just a shared secret system like TOTP then I've got great news, it's much cleverer than that. By not relying on secrets the system is robust against total incompetence by a relying party. If say Facebook paste all the U2F credentials they have for your account into a public Pastebin, not only can that not be used to attack your Login.gov account secured with the same FIDO key, it can't even be used to attack the Facebook account the credentials are for.
Military intelligence services actually rely heavily on analysis of public information. The value of the exciting and expensive Hollywood-style secret agent is mostly in their ability to do stuff, mostly illegal and immoral stuff, not a benefit to collecting intelligence.
Open source is useful, to be sure, but so are informants / agents, and the safety of those sources and their continued usefulness is completely dependent upon secrecy. If that's too Hollywood then consider undercover law enforcement.
Society blurs this line a lot by telling people things are "Private" when in fact they're only a secret, and then there is an opportunity to betray them. This happens for payment cards for example, bank representatives have been known to tell even a court of law that bank employees can't find out your PIN, so if a PIN was used it proves the customer was negligent or actively participated in the transaction. In fact, of course, the PIN is a secret, so the bank and thus its employees are aware of the customer's PIN and an insider could in fact perform transactions using PIN verification despite no negligence by the customer.
I'd be interested to hear how you think law enforcement and intelligence could still work without confidentiality.