Two different things: the first is the way we simulate an attack and the second is how we atemi.
When I'm at home (i.e., not visiting), I vary my attacks. Sometimes more the horizontal fist, sometimes the vertical and sometimes the old bare-knuckler method. I always try to strike with either the two largest knuckles or even just the index finger's knuckle. On reflection, I also sometimes use the #1 atemi described in the next paragraph. I also always try to keep my back hand up in a realistic guard position vice down by my hip.
Our (hand) atemi, subject to all the cavaets of failing memory, ignorance, etc., is of three kinds: 1. Middle knuckle protruding with fist palm up and elbows in, 2. Shuto (actually the outside edge of the palm vice the side of the hand and 3. Palm/palm heel. Each is used on appropriate targets for effectiveness and to limit damage to the hand.
BTW, we also knees, elbows and the very, very rare kick (I can think of only a couple of instances...both are from a sacrifice throw counter technique).
When I'm visiting another dojo, I closely observe and try to do what they do for both attacks and atemi. A. I see no reason to attempt to interject my thoughts, prejudices, etc. into their practice. B. I might see something way better and C. It's just the polite thing to do.
If you'll allow me to wander a little....
This gets into my philosophy about what aikido is. Now, this is my personal philosophy and doesn't mean it even reflects my instructors' philosophies.
In short, I believe that aikido is about constant improvement.
I think that I should always be honestly evaluating my technique. As nage/tori/sh'te, I should be looking to eliminate holes (e.g. chances for uke to counter) in my own execution, looking for ways that I can slightly change my technique so that uke has more holes in his position.
I should be looking for those situations that allow me to practically bring conflict to a least-injurious-to-all (with me and mine first priority) resolution.
By technique, I don't just mean once uke has grabbed, punched, or whatever. I mean the whole context. Particularly maai and subtle body positioning and movements that put uke into a inferior position even before the attack has commenced.
As uke, I believe that I should always be striving to provide a better learning situation for nage, always looking for a way to move that limits my holes and preserves my options to counter and to, finally, take a safe fall.
I believe all that is _very_ ambitious. But, I believe that's just part of aikido.
I believe that my aikido has to be effective. That's the baseline that I use for differentiating correct from incorrect. OTOH, I believe that for me the real applicability of aikido is using it for self-improvement.
That's my story and I'm sticking to it. Till I change my mind.
Sorry to ramble.