I love when waza are peppered with a few atemi -- I can think of one Sensei in particular that would whack you at least three different ways during each technique. But my Sensei does not emphasize it except among the most senior students. I suspect, without knowing for sure, that for most of us doing an atemi takes nage's focus away from flowing, connected technique.
Yes we all know that aikido atemi is supposed to startle uke and corrupt his/her center, but in my case at least, often when I actually try it as nage, the rest of my technique degrades.
So I am on my Sensei's page and will get into atemi whenever he starts emphasizing it for me.