Good topic Robert,
I think the problem is that as aikido "evolved" there was a split. Somewhere along the way atemi was, for the most part, removed from the equation. Many aikidoist now think atemi is something additional/seperate from a technique, an "optional addition", or something along those lines.
I question my aikido training, the way it is taught and how I practice it. I think this is healthy. Wish to train to deffend myself against the attacker that is stronger, faster, has better balance and speed, those are the people I need to worry about. If atemi provides me with a defense and an ability to defend myself against the aforementioned foe than that is what I want and need to learn to feel confident.