The student of modern aikido should understand that it did originate, after all, from arts that were designed and practiced by samurai—professional warriors, whose job it was to kick some serious ass. Now, for the most part, punching or kicking didn't do a whole lot of good when dealing with an opponent wearing armor (hence the predominance of joint locks, throws, choking, etc.), but samurai were occasionally called upon to deal with violent situations while dressed in their civvies, so why not add the proverbial insult to injury by cracking a rib before you pin him and politely separate his head from his shoulders.
But Ueshiba turned all that into an art of love and peace and harmony, right? Well, for one, Ueshiba did his fair share of atemi in his practice, but yeah, if that's you're approach to the art, and you'd like to refrain from doing something as barbaric as cold-cocking the guy, splendid.
And yet, it does pop up occasionally, as I mentioned, in the koryu kata (as far as Tomiki aikido goes), so it bares contemplating. Now, it does serve a purpose, but my concerns lie not in the why but the how.
Punching for realz
I'm by no means an expert, but I've studied enough Shotokan karate to know that there's a right and a wrong way to strike someone or something. Do it incorrectly and you're likely to hurt yourself as much, if not more, than the other guy.
So if you're going to keep strikes in your kata, beuno—but I would advise learning and practicing how to do it correctly, not to mention where to hit the dude. Alternatively, as many in our system do, the punch can be replaced by a simple shomen ate. It seems to achieve the same thing, it's in line with what we've already been practicing for years, and perhaps more importantly, uke doesn't get his bell rung over and over.
Do or do not
I'm a firm believer that what you do in practice is what you'll do in reality. In other words, if you practice the atemi in such a way that you feint the hit, or "stop short", that's more than likely what will happen "on the streets."
If you tell yourself that, "Sure, when I train, I pull my punches, but in a real fight, I'd really hit the guy," I suspect you're in for a bit of a surprise. That's a conscious decision, and fights often boil down to split-second, gut reactions—the subconscious. Which means, if you want to include the idea of really hitting someone in your training, you need to really hit someone when you're training.
This, as many martial arts can attest, can prove problematic. Most people don't like getting punched over and over, be they bad guys or friends and training partners. Which is why sparring gloves and protective headgear were invented, so that everybody can practice doing violent things safely. (Am I the only one that finds that idea somewhat ironic?)
Of course, sparring gloves can make it a bit difficult to perform any of the finer hand movements often required in aikido. Maybe use those padded, fingerless MMA gloves?
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Ultimately, I'm not here to make a case for or against the using of atemi in aikido. I'm just urging folks to be realistic about it. Never forget that, while we will spend 99.9% of our time doing this stuff in a nice, safe dojo, with friendly folks and pre-arranged forms, etc., any martial art is fundamentally about very real, very violent, very dangerous situations. Even when used in the spirit of love and peace and harmony, chances are very high that someone is going to get hurt, sometimes badly. Better them than you.