UI customization has to be built from the ground up so that it works with the rendering engine. World of Warcraft's UI is based around XML and MxOs isn't.
Also recall that World of Warcraft was I believe just ending Beta when MxO release so it wasn't all the craze yet.
The Zion mainframe is what you may be refering to the reason it was technically against the EULA was it involved having a bot account that you sent private messages to.
Also City of... might have a slightly different EULA then SOE's so its possible that Hero Stats and such dont violate it. Or they simply can't detect the app because it runs totally client side so there is no way to enforce something against those that use it.