Nope have to leave them plugged in for the easiest experience. Not too bad really, if you have the space. I have 3 GameCube controllers on a rack mounted the the left side of the ent. System, two snes usb in the middle rack of Munich rackmount part of the ent. System, two xbox360's on the right side rack, PlayStation controllers on the top of a PlayStation 2 stand, and all 4 wiimotes on top of a wii stand.
Yeah it lools like a lot , but it's not that bad or hard to have set up. Hardly ever have to remap, unless something gets unplugged accidentally.