I'd never heard of this. It's a fun thing to think about, but of course unethical and also a bad idea for obvious PR reasons ("LINUX IS A VIRUS!") to actually do.
Many people wouldn't notice possibly ever, at least until someone technically literate looked at it and told them what had happened. Why would they? They'd just think it was a normal Windows update that included some UI changes.
Now, if the virus's autoconfig was poorly written and gave them a broken setup, they'd certainly notice something was broken, but would probably blame Microsoft ("Windows Update broke my computer!") . There's no need for them to write their own autoconfig: KNOPPIX's almost always works, so they could just use that.
As long as everything works, they'll just adapt to any UI changes, because they'd assume Microsoft had pushed them out, this UI was the latest version, and the path of least resistance is to adapt to the chance rather than fight it. The reason some people throw up their hands and get so whiny over minor UI differences between Linux and Windowsis is because the path of least resistance is to reject any optional change to their setups.