I think Section 31 was handled poorly in recent Trek. In TMBS everyone seemed to know about them. They operated a bigass space station and gazillions of ships and even ran around Starfleet vessels with their own black badges. And now in PIC they store their stuff openly at Daystrom Station. Sure, the station is top secret but one would think that S31 had its own concealed storage and didn't rely on the civilian Daystrom Institute. It just feels likecurrent writers didn't bother to actually watch DS9 and see what S31 was really about.
I think there's enough wiggle room with section 31's presentation of Section 31. Starfleet command knew of them (didn't deny their existence to Sisko, gave him the runaround when he asked them about it), Admiral Ross worked with them. So clearly they were known. Maybe not to the average Starfleet officer, but the higher ups at Starfleet knew who and what they were. Starfleet even agreed with their tactics (genocide) by not providing a cure.
DS9 is over 100 years after section 31's appearances in Discovery so them being known in the time of Discovery doesn't necessarily mean they would be in the following century. I wonder how Riker found out about them.