With the Apex Neptune, its easy to control to turn off the lights if it exceeds a certain temperature limit. It also sends out an email.
If you have the iSocket (environment version), you can plug in a temperature sensor - it can then send you an SMS & power off the plug (connected to lights?) as well.
I'd always keep the wavemakers on - they provide circulation & oxygen for fishes/corals. Never turn it off. They don't give out much heat anyway.
And to take care of drop in salinity due to skimmate removal, this is what i do for longer trips - Aqualifter pumps skimmate into a large container in the sump. The water displaced will maintain water level such that the ATO only takes care of evaporation only.