I've just listened to a podcast I found on itunes last night. It was an interview with Ellis Amdur. He said according to him, the atemi in aikido forms is usually an extension of the arm or running the arm along uke's limb. An example he had is in nikyo, tori could come down with an elbow strike.
I see some of this aspect with my sensei. When I have to receive kokyu ho I usually have to keep my head close to his arm. If I don't he would hit me with his elbow (and from my reaction he could then throw me easily). It's similar with irimi nage. If I don't move, he could just strike my face with his fist while pulling on my collar to make me throw myself.
In the book best aikido, there's also some explanations of the use of atemi with the doshu punching uke's rib as he enters for irimi nage. It's also worth noting that he used a vertical punch (like a tsuki movement).
In uchi kaiten nage or uchi sankyo, there also seems to be a variety of atemi ranging from an uppercut punch, a wave of the hand, a palm smash to the chin or a vertical punch. I don't think it matters that much if what you really want is to get on with the technique safely. Atemi from the bottom of the face seem more effective martially though as they are harder to see coming.