Section 31 in Into Darkness was still pretty hidden. Kirk and no one else on the Enterprise seemed to know about it.
No, just the thousands of analysts employed in their massive London facility alone, not to mention the engineers and workers building their secret super-ship (or not having a problem with the secret super-ship being built for Starfleet not being delievered to Starfleet but instead to this sketchy third-party group), the crews of the ships they had combing the galaxy for sleeper ships full of augments or whatever, and the support staffs for the same (I don't think you can just pull up at K7 with your secret black-ops fleet to top off the antimatter tanks without getting a few questions) knew about it.
DS9 and ENT suggested that one or two 31 agents on a ship or starbase was a lot, (not unlike the concept of four Changelings in the Federation causing incredible havoc) and STID showed them basically having their own parallel Starfleet, operating totally in secret despite being an unbelievably massive organization.
Now we have DSC showing that 31 agents were working as security guards? In the open, identifying themselves as such to everyone who could see them, where there'd be absolutely no benefit to making them appear to be anything other than standard redshirts (and where, indeed, using redshirts for guard duty where no special knowledge or tactics would be required would make a ton more sense. It'd be like if James Bond was operating a metal detector in the lobby of 10 Downing Street instead of doing something requiring his level of expertise, while wearing a double-0 lapel pin). Again, it's trading on the cachet established by DS9 to make the mundane seem badass, or the unbelievable seem plausible, without actually understanding what was going on in those stories on more than a superficial level. At least STID had the excuse of being written by a conspiracy theorist who'd be predisposed to not think "secret, parallel Starfleet that real Starfleet is just a front for" isn't ridiculous.
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