I've been able to find the N-girl in the e-gacha box for a while (for the last four or five events). However, until the last event or so, when I already had her she didn't keep showing up in there. Maybe that's what's confusing you? The N being there isn't really a problem though, it just takes the place of a rare.

The N not being in the N-Gacha is a problem, absolutely. Thankfully they just screwed that up once and haven't kept doing it.

The N doesn't muck you out of any SR's though (if you had the step-up image, it is because they've got some really stupid logic in the game that makes it appear sometimes when you roll "all silvers"-- and an event-normal). It didn't reset your counter to get an SR though, if you look. Just wastes the card reveals. Which, I also agree, is annoying.

At EG they put Wako in Event gacha, when she was shouln't be useful for events. They released it again to N gacha once i spit the screenshot on their FB

And is a problem, Event gacha cost the same than R gacha (ignoring daily deals) and has a worse success rate for everything (because joins cards from N gacha + cards from R gacha + exclusive cards from event gacha). At least R gacha guarantees R cards.