They might now be (officially) disavowed and disbanded (plus Control killed a bunch of its operatives) but kept running in the background as a total black ops as opposed to more a more publicly known type of organisation. Think a "Men in Black" type of deal vs the CIA. And remember, there's a hundred years between Disco and DS9. An organisation that officially stopped existing a century ago and doesn't have a paper trail wouldn't be something widely known by people.
One of DS9’s episodes had Bashir stating that Section 31 had been hiding in the shadows for three centuries.