I believe the issue is that Amazon and others specifically forbid affiliates from overwriting or replacing other affiliates links with their own.

But yes, you are correct, some of the more "successful" (if you can call it that) Windows malware has taken the form of IE6 browser plugins and toolbars that overwrite affiliate links in any page you browse to. I can seriously imagine some enterprising 16 year old somewhere in Eastern Europe making 5-6 figure monthly income from this back in the early 2000s.