my experience is that Atemi as a "mind catcher" has to reach the awareness of Uke.
Some people have good reflexes, they can sense a hard and fast atemi and react properly. Some people haven't been kicked in the head enough to have that reaction time. the typical result with those folks of 'benevolent' atemi is that they'll ignore it (as if it they weren't providing openings).
As nage you can time your atemi so that the lightbulb goes off in uke's head (shit I'm open) which ultimately gets uke to move into the technique. Surely you've noticed that usually uke's best defense path is the ukemi for the techique..
So sometimes atemi can be more effective slowing it down than the other way around.
You're probably right that striking shouldn't be something that allows for this reaction; but if that were all there was to Aikido technique then most technique wouldn't be required; I mean there's such an opportunity for mayhem all through the course of any technique ..
..ugh don't mind me..