Sure. An analogous application of secret policy working within the framework of a law that delegates huge amounts of authority to the executive would be military strategy. Another would be FBI investigation priorities.
If you remove the "secret" constraint, but keep unilateral authority to do rulemaking without line-item approval by Congress, you can come up with zillions of examples.
I think you're implying that the FISA court's keeping the basis for its legal authority secret is analogous to any independent federal agency making statutes in accordance with its congressionally granted authority. I think the critical difference is that in the run of the mill federal agency case, the source of authority to make rules is clear and a citizen's legal recourse if he or she disagrees is also clear. In this case, one can't sue the federal government for violating the constitution because one doesn't know what's its stated basis for constitutionality is.
It's hard not to conclude that the FISA legal reasoning is secret because it sucks -- it's weak and at best unorthodox. In other words, most people qualified to have an opinion would think its not sound -- i.e., not really legal -- i.e., it's an unlawful power grab. That's one way a democracy might turn into to something entirely different. Really!
Is there the rule of law in the U.S. or not? Are FISA judges subject to the rule of law or do they perhaps garner their authority from a divine source like the Kings of England? Or maybe the chief justice's left testicle? Or is it righty? We can't really tell. And we can't really tell whether we live in a lawful state or not -- because, in this case, it's a secret. Severe coughing fit followed by a mournful sigh.
It seems like if one's answer to the question "what is your legal authority?" is "it's a secret" then you really don't have any legal authority and are deriving your authority from some other source, whether you'd like to admit it or not.
Further -- can someone tell me if this is a new thing? Is there any legal precedent to the law itself being secret?