Is Aikido atemi and SG only effective in it's full extent on relatively seasoned fighters?
Possibly, but I don't really think so.
If you look at most dojo situations the beginner is pretty darn safe. Everybody's been really nice to them, is taking it rather slow and not trying to injure them or let them injure themselves. We ask the beginner to "pretend" we are going full speed and that they really attacked us and this is a real situation and to act accordingly. But it's not real, it's pretend. I think if you were to take that same person and stick them in a truly threatening situation you would see a marked improvement in their awarness of physical danger and their reaction times.
The short of it is that most beginners aren't expecting to get smacked/hurt/atemied
or whatever, so they're not even considering that they should be looking to defend against something like that. Once they know that if I can touch there face I can hit there face their awareness starts to come up.
But that's just my take.