I do recall viruses/worms on early implementation of usb - the early cards, as well as sometimes came out with it from factory - as early as on win 98.
Most was only working on windows - they were trying to execute ie activex code;
There were plenty of attacks on early intel me, but no1 was talking about them.
The oem attaching spyware, having built-in backdoors, and Trojans pre-installed was quite common back then too.
In short nothing has changed, but everything kinda went quiet during war on terror. Either gov moved to more sophisticated ways to penetrate systems, or they cracked down on them; but Windows 2000 pro (NT) platform made it much harder to execute code like that too.
(If one belives forum talks on warez forums like astalavista back then, would recall choppers flying over houses with magnet like/antenna attached - activating chips - and systems would proceed to download magic files...)
(SC also had chipped motherboards for servers that were calling home to china sometime ago)