Who would win?
Zak. Rex's nanites can disable Ben's Omnitrix, but they can't disable Zak's powers.
Zak can control cryptids, some of which are gigantic in size and have various powers. Rex can create anything he can think of with nanites. Both of their powers require concentration to work. However, Zak is more focused than Rex, judging from what I've seen of both of them.
Aliens, E.V.O.S and Cryptids
If your using 16 year old Zak Saturday in this debate, shouldn't you use 16 year old Ben Tennyson ?
I do not know if nanites can disable omnitrix. If they don't, Ben is clear winner.
With Omnitrix being a Device Leauges above Nanites. Don't think so, Also Ben could just turn into upgrade and disable Rex's powers or use Rex as his slave for the battle
Since you didn't ban Alien X, Ben goes Alien X and wipes Zak and Rex out of existence.