Well, if you don't want to look at the other windows, there's nothing stopping you from setting the resolution to something tiny, and leaving them in the background. If Warden doesn't like wow played from minimized windows, there's plenty of ways to not look at windows yet still not minimize.

But yes, hotkeynet can send keystrokes to minimized windows AFAIK.

And if I were a botter, I wouldn't multibox bot. I would keep em all solo, on separate machines (not that i'd ever bot anyway, why pay for a game just have your computer play it?). Why take 2 things that people can obviously see and report you on and increase your risk? That and xp loss due to grouping would slow down botting, i'd think.