Hey, no flames!
Yoshinkan aikido has atemi in almost all of the 150 basic waza. We tend to be a little anal about form, so we tend to practice atemi every class, as we practice the waza. Kind of goes hand in hand.
One of the branch dojo I used to train in used Bob Bob the punching Bob as well as heavy bags, and such to practice striking. I've seen aikido dojo with makiwara as well.
By the by...I've seen really good aikido without a lot of atemi, and I've seen really bad aikido, with a ton of atemi, and I've seen really good aikido with a ton of atemi...
Everything is relative...