There are really
only two types of atemi in Aikido... the one you see most often is going to result in nage splitting their knuckles, breaking their fingers or knuckles, or giving uke a slight pause - the second and more elusive beast is a properly timed atemi.
There is a tendency to use atemi to the face to prompt a reaction from uke, and if that is your intention (to more or less take them off line or take their balance) then this is all good. If you want to make the strike work then you need to aim and time your strike with much greater accuracy.
Ron is right that the atemi that uke does not see is the clear winner. This is true whether you actually land the atemi or not.
A lot of other factors such as the distance between yourself and uke have a huge bearing as does the direction you are coming in from.
I come from a Kyokushin background and can punch, elbow, knee, kick, strike tetsui or uraken very effectively from just about any range. What I've learnt since beginning Aikido is that those same strikes can have just as much of an effect on nage as uke. Strikes that are rounded in origin, highly vertical, require a lot of hip movement, etc. can really throw off the rest of your technique.
Strikes to soft tissue points whilst passing are not likely to knock your uke out, but can give you vital seconds to perform a technique. I watched a BJJ-style class before our class during the last week and watched the instructor try to atemi before moving in on his opponent. He struck his fingers against his opponents knuckles on the way through, pulled back and spent five or six seconds shaking his very sore fingers. Interesting to watch.
Remember as well that everyone reacts differently to an atemi too. Before beginning Aikido, and probably one of the major factors I started Aikido, involved a very serious fight with a family member (ex-military). His first punch to my face snapped my head backwards and off the brick wall he had me pinned to. All it did was make me madder - it didn't slow me down and I'm not as hard as some of the people I used to train with.
You're right that atemi is a fundamental part of Aikido in my opinion (sorry to the people who don't practice it) but its an interesting path to follow and to try to stay true to Aiki principles.
Best of luck with figuring it out