My early aikido training included soft atemis (to prevent injury), though it was necessary for Uke to 'block' them with a hand to stop himself getting constantly poked in the groin or slapped across the face.
However, on a recent course I noticed the instructor was very averse to Uke blocking atemis (and therefore they were even softer or not even touching). Obviously I found it nearly impossible to get out of years of habitual atemi blocking. But the instructor had a point. He said that it 'closed' the Uke (and it also prevents uke seeing what Nage is doing in many cases). On another point, is it realistic to expect that someone could block an atemi in a real situation. (My view is yes).
What do you think; block an atemi and have a closed Uke or don't block and risk pathetic atemis being exhibited and students developing no quick reaction to small atemis?
My opinion on this is as follows:
a) all atemis are a way to point out an "opening" in your partner's guard (in fighting I don't care whether he knows he's open or not the atemi isn't there for his benefit). When I started Aikido under Saotome Sensei, if you didn't protect yourself by closing the opening you got your nose flattened. Only a couple of those and you got the picture and covering your "openings" became automatic. As far as I am concerned, training your students not to cover an atemi line is traiing them to be stupid. As you commented, when they don't respond to the atemi the partner has to pull the strike or not do it at all. This is just plain dumb from a martial standpoint (the instructor may have some "spiritual" reason for doing this). Once you stop doing atemi your begin to get unaware of the atemi that can be thrown at any instant by your partner.
As I stated in one of the earlier threads on atemi, Saotome Sensei taught us that if the attacker knew he wouldn't be hit, all techniques are stoppable. It is precisely the need for the partner to be aware of and to praotect himself from the atemi that makes all of the techniques in Aikido that we use to end a confrontation possible.
That said we cxome to the second half of the issue:
b) "blocking" of the atemi also makes no sense. If by blocking you mean merely stopping the incoming blow wothout any additional change in the relationship between the nage and the uke then it is equally stupid from a martial standpoint. At the beginning of our Aikido career we are working on our basics. Training is quite structured in order to make the principles as clear as possible by artificially isolating them for study in a way that would never be so simple in real fighting. The first thing Sensei taught us was that in real fighting, weapons as well as empty hand, there are no blocks. Everything is a strike that we are choosing not to do by way of practice.
In a martial context the attacker will attempt to counter any atemi thrown at him by deflecting and counter striking in one motion (offense and defense are one - a key principle), or he will actually deliver an atemi to the limb delivering the atemi (the Kali folks call this "defanging the snake") and then following that up by moving in to the resulting opening with a followup atemi. When I say an atemi I include any lock that can be applied to a joint in an impactive manner as part of the defelction of the incoming atemi. The Wing Chun and Jeet Kun Do folks will use trapping techniques to neutralize that opponent's ability to counter by tying up his limbs.
Any Aikido practice that is really trying to incorporate martial principles needs to allow for the nage to defend himself in this manner. You can consider your technique to be effective if he tries and is unable to counter your movement using these means.