I knew a guy(Elysium server), who changed textures for floor in C'Thun's room and made "hole" into AQ40, that allows to enter C'thun encounter in less than minute.
He was banned few minutes after login, even before he moved to AQ40.
So, Warden works pretty good, even for 1.12.1 clients...
At least, how I understand its methods:
server knows signatures of ALLOWED mpqs(and other files), so any non-listed mpqs will result in ban. Also I remember some posts from Nostalrius where players asked GMs to add improved models mpq to allowed mods.
P.S.
Nostalrius:
How about cheats ? Blizzard Warden has been implemented (yes, it's the retail anti-cheat system), with the checks against the latest known cheats. The main thing is that this system can theoretically detect any cheat (from MPQ/DBC modifications, to packets modification, including memory modification and proc detour ...).