Not Hitler Jugend then, not by a long shot. Evil, ruthless supermen, yes. But not a well-organized movement of them.
You're being too literal. Of course the augments are not an exact 1:1 analogy of the Hitler youth, but it's a very strong and obvious connection that was being drawn, and visually, making them blonde and blue eyed in Khan was done for that purpose.
From a matter of human rights, the issue is basically the same. Hitler believed that genetic perfection was the key to human development, and that if you can prove your genes are better then the next guy, then you are entitled, by birth, to be above others. That's the running theme. This is a common thread in Trek, that you should be respected even if you're handicapped (Geordi being blind) because you may have other qualities unique to you as an individual.