Yeah, Harry could have ended up working
for Nemesis without being Nemfected himself, by working for someone who
was Nemfected (such as Justin or Maeve).
Which doesn't necessarily mean that Harry
is immune to Nemfection; that's his own guess based on what Eb says - Nemesis could be somewhat different from a "standard" Outsider.
As well as the 2000 year in the know Woj about Nicodemus compared to this 666 year cycle.
I don't think that's really contradictory. Nic is ~2000 years old, and so he's seen the cycles before and understands them. That doesn't mean the cycle length is 2000 years.
From here:
https://wordof.jim-butcher.com/index.php/word-of-jim-woj-compilation/woj-on-vampires/Lord Raith is "a couple thousand years old. He’s got 2 thousand years of paranoia kinda built up" so roughly the same age as Nicodemus, and "There’s kind of a long game going on in the Dresden Files, and Lord Raith has been involved in it in the last couple of cycle’s it’s gone on."
So that seems to fit a 666 year length, since Lord Raith would have been around and already old and powerful for the last two events.
EDIT: fixed incomplete sentence