> And finally in Discovery, it was a known, fully legal branch. That Discovery also took place before D.S.9. made it all the more bizarre that most Starfleet officers in D.S.9. had never heard of the existence of an organization which was publicly known a century prior.
Discovery was a deeply classified ship that was further reclassified under Klingon War Intelligence, Prime Directive, the unspoken Mirror Universe Prime Directive, and Temporal Prime Directive due to various actions Discovery has taken part of over the course of its deployment.
Supposedly no one on DS9 ever heard of Discovery (or should have heard of Discovery) either.
So it's not entirely unfair for Discovery to have a lot of deep, direct knowledge of Section 31, more than most ships and crews would have, given their existing high classification level likely meant they had high clearance in return. In addition Season 2 offers some evidence for why Section 31 was nearly destroyed and likely went into hibernation through most of the TOS and TNG years, including the death of high ranking officers, a ton of institutional knowledge in the loss of their computer files, and the extra-temporal extrication of the person most groomed to likely take over the organization (Georgiou).
(That said, I still think Section 31 is one of the dumber things added to Star Trek lore, and the DS9 writers can complain all that they want that Section 31 has been almost nothing but misused from their original intentions since they created it, but it is the DS9 writers' own fault for retconning Section 31 into the Federation charter in the first place and not expecting for everyone working elsewhere in the timeline to wonder or be questioned "What would Section 31 be doing right now?")