Due to the Red Angel situation, Control existed at various points in Galactic history; and it was even stated in ST: D that Control could have hidden parts of itself and could re-emerge. Yes, Burham and Co. took the Sphere data that Control was after to the 33rd century - but that doesn't mean Control was completely destroyed (if they could have confirmed that, they would have no reason to take the Sphere data to where Control would never get it.)
So, yeah, somehow the Vulcans (before Surak's time and the Vulcan/Romulan) found out about the possibility that Control would end all life at some future point, and created the Zaht Vash to see that Synthetic Life would never exist <--- And that's why we have BOTH Vulcans and Romulans working together in STP to stop what they see as an abomination, and something that will lead to the end of all life in the Galaxy.