Grub,
I do not have the inside details on how the Hunter controller works, but most systems are very much the same.
The timer functions and settings are managed by an embeded controller. This controller is typically run using low voltage logic levels like 5 volts DC or 12 volts DC. They are also isolated from the valves using independent high current transistors.
Based on your information, either the high current transistors took the hit from the lightning and fused two zones together, or out underground somewhere two valve wires were fused together by the high current generated by the lightining strike.
The easy way to figure this out is to remove one of the wires from one of the two joined valves right at the controller and run the system.
If the second valve still comes on, then the wires are fused somewhere down the line. If the disconnected valve does not come on, then the short is most likley in the high current transistor module. Some of these are replaceable and some are not. I would check with Hunter.
Warren