I also think it might be a bit difficult to read, but part of that is that I'm not on much of a grimdark mood lately.
My big questions are of the Nazi strategy- what do they do now that they're in charge, and how do they cover it up? For example, the Nazis are mainly known for genocide/massive human rights violations, but that sort of thing is hard to do without breaking cover.
And if you talk about how a government could do all that evil stuff secretly, it'd be easy to either get too real or risk sounding like a tinfoil hat. However, I think if you were willing to take more of a turn into politics, it could work out really well, though it would take a lot of work.
This sort of idea could give you a window into exploring the more universally condemned forms of human evil by using Nazis as a sort of framing device. However, I don't know how you'd wrap that sort of story up satisfyingly.
Another big question- who are the big baddies? Would any of the Nazis from that time still be in the condition to rule? Otherwise, would it be weird to have unknowns representing the Nazis?
I hope I wasn't too rambly. Quite a cool idea!

Nightmarish enough I probably wouldn't want to read it, personally, but it definitely doesn't sound too cliched. I think you'd have to balance how it is that people didn't notice (maybe some did, and then vanished?) with how subtle they'd be willing to be even at the risk of avoiding discovery...Also, in a hundred years, working with the assumption they'd be able to find new recruits to begin with, they probably wound up with some who nearly blew their cover by wanting to be more radical. If they were able to keep undercover for a century, it probably didn't go well for the radical recruits.

How are you thinking the world finds out?

~Z

PS: This does sound a little like Hydra, come to think of it--it didn't at first, but as I kept writing about it, it started to. Still, given the lack of SHIELD and superheroes in general, the story would probably have a different flavor...

PPS: My response is purely from a literary/historical speculation mindset. While I can see how one might go into modern political commentary here, I'm not trying to.