Atemi should be first and foremost a strike. This idea of a shock to the system so it becomes disorganized works best, in my opinion, in the form of a fist to the center of the face, under the chin, to the side of the head etc.This idea of spooking a person by waving a hand in front of the face is in my experience completely useless from a defensive point of view. You have to get in there and hit. Otherwise you are dead.
I agree a strike should always be ready to fire in an atemi...it's definately NOT just waving the hand in front of the attacker. I just prefer to not box in my set of options, so to my mind, anything which can be used to shock their system can be defined as atemi. Still, the bottom line is that we cannot rely on our attacker to cooperate with us, so we have to be prepared to place fist, elbow, whatever into the structure of our "partner." As an example to clarify where I'm coming from, when I don't respond to atemi at my dojo, I get hit.