It seems to me that O'Sensei emphasized atemi for training purposes. The purpose of atemi is to make sure that your postion is correct and that the opponent is unable to counterstrike. In such a case, you are now free and clear to complete the technique. If you are unaware of how and where to use atemi, it probably means that there are many weaknesses in your technique, and in a real-life situation your aikido would probably not work.
Much confusion arises because Koichi Tohei de-emphasized atemi because he felt that it interrupted the flow of the technique. In a way, he was right, especially for someone at his skill level. That's because his position was always correct and he was never in any danger. But, I suspect if he suddenly found himself unexpectedly open to attack, he would not hesitate to use atemi.
Atemi is an extremely important training tool, and everyone should know how to use it as such. In fact, some basic techniques cannot be done correctly without it.