From what I heard, it doesn't count clones; it counts the 4 units in your line-up only. Look on the bright side: at least Hidan does something else other than killing himself now.
Although, has anyone try this passive in rank battle/GNW yet? Does it count all 12 ninjas in your field?
Every times a unit in the field is defeated (both teams), his Ninjutsu and Attack will be increased by 12 %. It's a powerful passive skill if there are more than 4 enemies or there are some ninjas can resurrect (both teams)