I have a small commercial home shop, only 3 CNC machines. I always leave my machine computers powered up, and the machines E-stopped. It's my opinion that power cycling computers is harder on them than leaving them hot. On some machines the computer comes on with the control power, which in most cases also starts the hydraulic pump (if equipped) and some other hardware. On our machines, computer and control power are separate.
The air compressor is on a timer and shuts down at 9:00 PM, manually restarted when needed. We work odd hours, but the timer could be programmed to start at a fixed time also, just not needed in our case.
We run the warm up routines manually when the machine is needed. It would be difficult to automatically run a warm up for two reasons. 1) the E-stops are twist to release, and 2) the warm up program has to be loaded and run. With most CNC machines it would require some major rewiring and configuration to automatically override the E-stop and run a warm up program.
We normally run the warm up with a tool in the spindle, but I guess it wouldn't hurt anything to run the warm up with no tool in a spindle as long as the tool locked sensor is happy.
I think the most common way of having the machines ready to go at start of shift is to have an actual human come in early and start up the machines and run the warm up before the rest of the crew arrives.