If the possibility of thunderstorms exists, then you will want to power off MX, unplug D'ARC, unplug the B&C Interface Box, power off the CCD, and shutdown all computers. Be sure turn off the MX stepper power supply before turning off the Enterprise Z-80. Refer to the CCD manual for instructions on powering down the CCD and computers. Turn everything off if any significant work is to be done to the telescope or instrument.
Otherwise it is OK to continue taking biases, darks, lamps or flats while you sleep. The stability of both MX and the CCD seems to be better if they remain powered all the time.