The whole idea of augments in general is a social commentary on the Nazis and the notion of aryan superiority and their nascent eugenics movement. This was true in the original Space Seed even though the augments shown were not universally blonde. Certainly the casting choices to skew young, beautiful, and blonde, was the team at that time desiring to drive the point home a little too overtly, especially considering that Khan himself was not a germanic type.
I don't dispute that holocaust deniers have been around, but this is kind of a side-issue to whether the general public accepted the idea that the Nazi's believed in a master-race and in eugenics. I don't think there's ever been much debate about that, even among holocaust deniers, who are usually white supremacists who believe exactly that.
A few years after Khan, you had the Bond film "A View to a Kill" in which Christopher Walken had his hair dyed blonde (he looked a lot like Bowie at a time, who they preferred to cast) as an ex-Hitler youth bent on world domination not unlike Khan in a way.