Yeah, there is that. I haven't finished Nier: Automata yet, but that was certainly true for Nier: Replicant. But at least for the Nier series (I have no experience with AC), I honestly don't consider those to be NG+, but instead the actual intended storyline. At least with Nier: Replicant, it seemed quite clear there was more to the story and that continuing is what you were expected to do. The same goes for Ys: Origin, where you only get the "true" ending after finishing it the third time (well, I think you can skip one of the characters, but you need the third character's ending). That's not NG+, but it's similar.

The Yakuza series, however, doesn't work that way, at least for the games I've played. They basically just work as I described, you can play the campaign again, skipping some parts, and the intent is to go finish all of the side content you missed the first time through. Some achievements are locked behind choices IIRC (i.e. experience both consequences), but that's it.