It is not going to bother the quadstick.
If you want to turn off the LEDs and turn down the volume, you could load a simple configuration to do that:
The only issue you might find with leaving the quadstick on is the calibration may drift with temperature or voltage. Rebooting the Quadstick will recalibrate all the sensors. That config file will reboot the Quadstick with a 2 second long sip on the center hole. This config also turns off the flash drive so the LEDs won't flash due to disk activity.