Atemi is really tricky in aikido practice. Personally I feel that it's absolutely critical, but that the way it's used by many (in the US at least) is completely wrong. Atemi within aikido should be different from the kinds of strikes and impacts that one sees in karate or tae kwon doe for example and should generally be used at *the beginning* of the encounter. Atemi can be categorized as impactful or penetrating. Impactful atemi affects the body whole and can be used to create kuzushi or affect uke's structure. Penetrating atemi is done to cause pain or damage. Striking arts use both, but generally emphasize penetrating atemi over impactful atemi. Unfortunately, many in the aikido community also employ this kind of atemi (penetrating) and it's my opinion that it is a mistake to do so. I believe atemi within aikido is best used at the beginning of the interaction in order to position uke and/or create kuzushi, but then kansetsu or nage waza takes over the exchange. Certainly like Lynn mentions, these movements themselves can (and often should) have atemi like body dynamics, but that does not make them atemi. Too often I see atemi used in aikido to cover up sloppy technique. This kind of atemi is used later in the technique when nage realizes that they are going to be unable to complete their technique with the desired results. "Oh no, my kotegaeshi isn't working, what to do? I know, I'll hit them in the face!"
I'm sorry, but if the end result of your aikido technique is just to pound someone in the face for not falling down, you might as well study boxing, it will teach you how to do that much faster and with much better results. In this scenario, atemi is used as a conditioning tool (punishment) to train students to fall down despite poor technique. This kind of training doesn't help ANYONE, and it is not how the art was developed. Atemi in aikido should be part of the nage's movements from the beginning, and not something that's added in here and there. An excellent example of what I'm talking about is Kondo Sensei's demonstration of Ippondori (the ancestor of aikido's ikkyo). In this video
note how two atemi are used on the entry. Kondo Sensei's initial entry is impactful, disrupting aite's initial attack and positioning him to deliver a second (penetrating) atemi to the floating ribs. This is all within a cohesive framework that allows him to transition between atemi and kansetsu waza without giving up any control over uke. Note too, how the more critical of the two initial atemi is the impactful one. If that atemi was not successful, there would never be the opening for the second one. Some of you may not see the first move as an atemi, but rather an example of irimi. To that I say, "poo!" Irimi is atemi!
So as to your second question, I believe atemi must be taught from the very beginning in order for aikido to have any martial merit, but the atemi may not look or feel like what one is expecting.