The 9V battery in a Hunter controller has the primary responsibility of providing the ability to program the controller remotely. Face panels can be easily removed and programmed with a 9V battery without the need to be installed in its case or door housing. Although irrigation system's are low voltage they still require 24V to activate station valves or solenoids. The 9 volts the battery supplies is not going to be sufficient enough to run an irrigation system, therefore the battery is simply for programming assistance.
The lithium battery or CR2032 batteries in Hunter's Pro-C controller's provide power for assistance in memory retention.