Bashir admitted to "working" for S31, inasmuch as admitting he was working for/against Sloane, but that isn't sufficient to prove the existence of a larger organization. As I said, Bashir and Ross only worked with Sloane. Was there anyone in S31 other than Sloane? We never saw anyone.
Besides, the idea that S31 could hide for centuries is implausible. The idea that it could've emerged recently in the 24th century is more plausible.