This doesn't make much sense, what does the GPU have to do with the power being sent from the PSU to the motherboard USB ports (hub)?
There is no correlation between the two, the motherboard should have VGA and / or DVI ports on there it's self, taking the dedicated graphics card out will not affect anything except you will now need to connect your existing monitor to the motherboard VGA or DVI port or other for integrated graphics.
So it short, the USB hub /s on the motherboard will still work regardless of weather the GPU has been removed or not.
So therefore, your keyboards lights and mouse lights will light up since there is still power being converted from the PSU.