I can say by running 3 Rust and 1 Conan Exiles servers that the Valve Anti-Cheat system is installed on the person's computer and finds cheats that way.
It is by the BattleMetrics system that I have recently (in the last year) VAC banned players banned from entering my servers. Though, one has to set up a trigger for that. So being VAC banned may or may not work with how W:ET servers are set up. Which I know zero about.
I'd "guess" at some point it would go over to SteamCMD for dedicated servers. It is much easier to keep everyone on the same version number and such, there. Even if it doesn't, I'm glad to see it finally on Steam!