Yeah, if the core FAH core priority is set to idle, which is default, FAH will back off whenever a more important process is present. I do mpeg4 compression with FAH running, and it takes the same amount of time if FAH was off. Sure, my frame times get murdered, but it yields to more important processes.
Also, if you watch task manager for a while, you will see that how FAH will jump anywhere from 0-100% while another heavy duty process is running. FAH will use any spare cycle, for example, if your rendering is pausing for some I/O operation.
So you should be fine leaving FAH running 100% while rendering overnight.