I am currently researching a book on atemi in aikido. I originally started it as an article but found so much stuff that I feel it is worthy of more in depth treatment. A few comments:
1. Historical roots trace atemi in the locking and pinning arts back to India
2. O'Sensei's training roots appear to provide a solid foundation for the use of atemi.
3. O'Sensei can be seen in most pictures delivering an atemi while delivering technique.
4. Technique can be smoothly applied without stopping to strike-in other words the strike can occur in the process of the flow of the technique without disruption.
5. Atemi waza is generally best accomplished by striking pressure points to cause pain compliance for setting up a techniuqe, or shutting down the muscle function to a limb.
6. Atemi or pressure point manipulation (kyusho jitsu) makes it easier to apply a technique.
I believe a strong case can be made for the application of atemi to aikido. A survey I performed indicates a lot of interest in the topic.
Dr. John Riggs