Typical paranoid thinking. Oooh, the conspiracy is all-powerful and smarter than everyone and they've fooled us all, oooh! Rubbish. No conspiracy lasts forever. No secret can be kept forever. Maybe a finite group of people can remain committed to a finite secret agenda for a particular length of time, but eventually people will retire or die off and be replaced, circumstances will change, mistakes will be made, and either the original agenda will be exposed or the people who cared about preserving it will be replaced by people with different goals -- or simply with less competence at keeping secrets.
Heck, usually whenever there's a change of leadership in a government or organization, the first thing the new folks do is try to make a fresh start, to clean house, perhaps even to make a name for themselves by openly cleaning out the corruption and mistakes of the old regime. It's naive to treat a conspiracy as some kind of self-sustaining perpetual-motion machine that can remain unaltered in its agenda and power even when all the people who were originally behind it have retired or died. The only reason most imagined conspiracies like the Kennedy assassination never get uncovered is because they never existed in the first place. Real conspiracies like Watergate and Iran-Contra tend to come out within a few years. Because it's really not that easy to keep a secret in a democratic government with a free press. If anyone is doing something sneaky and unethical and illegal, it's a cinch that their political opposition would gladly expose it and get them thrown out of office, and that the press would gladly investigate it because it's an irresistibly hot story. The only thing that would get all those people to play along with keeping the secret is national security. And even then, there would eventually have to come a time when the security needs had passed. It's only in locked-down dictatorships that detrimental secrets can be kept from the people for a long time.
So if anything, it's implausible that Section 31 even still exists at all in the 24th century. Any remotely realistic portrayal would've had them exposed about a hundred times more quickly. The only way I can buy S31 continuing to exist is if they've been mostly inactive over Federation history. I always figured they stay pretty much dormant in peacetime and only become active in times of major crisis like the Dominion War. But the past few years have been so fraught with one crisis after another that S31 has become a lot more active, and that just makes it all the more inevitable that they'll be exposed.