Almost all these comments and I include myself among these respondents, are irrelevant to the original question. "Did the founder take out atemi in Aikido?"
In response to Jun and Craig, there are some "strong leads" in the taigi, which I would call atemi. In particular there is a back fist strike, which I have been told is a "lead" because you roll your fist, rather than just letting it drive through the other person's face. Of course you pull back your fist before you actually hit.
I am assuming that a nage would use an open hand to indicate a strike during the execution of a technique. This would indicate an atemi and help maintain correct ma-ai. However most people just do the technique and don't indicate the atemi. Many times, doing the strike breaks up the motion of the technique. In some techniques, the atemi has evolved into a stylized movement.
I'm going to start asking around. Perhaps I'll find something worth reporting.