Is this surprising? Classified missions happen all the time in the military. Any potentially dangerous information is probably kept on a need-to-know basis.
Star Trek was more Athens (an open society willing to deal with the risks of being an open society - see Pericles' funeral oration) than a paranoid postwar nuclear power. There were some secrets, but the federation was constructed around openness, trust, and free exchange.
It's saddening that we now take it for granted that governments of, by, and for the people regularly keep secrets from them on the grounds that they "know best." It is hard to see how a democracy can really work when the population is so easily kept in the dark whenever governments play the national security card.
As a writer, it is disappointing to me that you appear to accept such "realities" so casually. I'd recommend reading books like Bomb Power
by Gary Wills which discuss how our sensibilities about gov't policies have been warped by perpetual "exigencies" which have licensed all sorts of secret programs.
One thing I give props to TNG narratives for is there exploration of the dark side of privileged secrets in the name of security.