You're thinking too much about it Kishi wasn't happy in the last interview with all the NH fan mail overating Hinata and bashing Sakura. It's pretty obvious he's not interested in making NH canon in his manga with the huge lack of development between characters along that Kishi has proven that Naruto will always love Sakura so Hinata never stood a chance.
Not only the anime deviates from the manga when a studio makes an animated adaptation like Ciardha said, Sailor Moon was a fine example of that, I remember reading the manga after watching the anime and I was like "WTF? This isn´t like the animated series at all, how they messed up the original work". But aniway, it happens also with manga adaptations of animated series. Evangelion is a fine example of that. The manga done by Yoshiyuki Sadamoto deviates from the animated series. Shinji isn´t as wimpy and spineless as the anime, Rei has a larger role and is more human, Asuka gets only a minor role in the manga (the changes made in Rei and Asuka are because the author strongly dislikes Asuka and likes Rei) and etc... So the changes doesn´t only appear in anime series but in mangas as well because the studios and mangakas have an enormous power and can do as much as they pleasse without respecting the original work. Kinda like what happens with movie adaptations from books.