I'm unsure any Towers were deactivated in Arena, although I'm still trying to figure out what became of the Jagar Tharn/Uriel Septim Enantiomorph. I think Numidium's status as a Tower was deactivated with the Warp in the West. The Red Tower and the White-Gold Tower's deactivation is pretty obvious. And I have no idea how the Snow-Throat got deactivated, if it even is deactivated. The Stone for that Tower is allegedly a "cave"; the Tower is also described as "sundered, kingless, bleeding" in the Dragonborn prophecy, but whether that means it was deactivated I don't know.
If the Direnni clan are allied with the Dominion, the Adamantine Tower is probably already done for. If not, it's got a great strategic position in the Iliac Bay and protection from navies in High Rock and Hammerfell, which will make it quite difficult for the Dominion to take it by force. Green-Sap was either already deactivated by the Dominion, or it's still a work-in-progress, since Valenwood is now part of the Dominion. I believe the Void Nights may have deactivated a Tower, as well.
What I'm wondering is, if the Thalmor do succeed in negating the existence of Talos, will he have the power of CHIM to hold Convention together regardless? And if all the Towers are deactivated and Talos no longer has a grip on Convention, is Mundus immediately unmade, or is it simply "unbound"? i.e. still standing, but with no actual supports and extremely flimsy