Whilst I actually mostly find USB very useful (and I really don't want to give up my USB flash sticks), a lot of USB stuff like mice aren't at all ESD tolerant. I would say that on every EMC test I've ever done, some piece of commercial USB PC kit falls over during the test. I'm talking about proper big name PCs with the factory supplied mouse and keyboard, not some no-name cheap stuff.

The default behaviour of the USB host seems to be to shut everything down if a glitch puts the USB bus into an illegal state. Unplugging and plugging stuff back in brings it back to life, which you may or may not find acceptable. It's a right pain in the backside if it interrupts your EMC test.