having two keyboards won't cause a problem using windows. The only possible thing I could think of is hitting the same "key" on both the arcade controls and keyboard, but I would imagine it would either just press the key or not register a key at all. That wouldnt really matter though, as I can't think of a reason you would have your keyboard out at the same time you were using your joystick/buttons.
The same would go for mice. You can plug in a PS2 and usb mouse, or 2 usb mice, and they would just control the same cursor, with the only problems occuring when you try to move both mice at the same time.