I will add that the "slice of life" sequence from episode 26 is very much a parody of "school life" anime/manga tropes. It was a short-lived thought experiment of a possible universe during Instrumentality.
As such, it is not much of a stretch to imagine that these scenes could be seen as actual in-universe anime. What I mean by this is, if NGE had been a live-action series, these scenes would still be 2D animation. And if the characters found themselves as anime characters in an anime universe (with all the expectations and preconceptions of anime characters), then blue hair would certainly not be out of place there.
(No more than the social convention of the girl next door coming to wake up and embarrass the horny male protagonist every morning.)