the hunter with "bird in the hand" doesn't attack air units anymore. (might try rebooting and see if its just me but I flew my dragon right into a cluster of idle enemy hunters that the A.I. controlled and nothing happened.)
Are you sure they had that upgrade researched? I was able to order my hunters to attack my own air units, at least, so I assume they would have attacked enemy air units, had I tested it in a skirmish with the AI not set to None (so I could do other stuff waiting for build/research times and recruitment).
