Haku wore Women clothing and hair style both on a mission and off a mission, a boy in girls clothing is not normal.
Normal or not.. I also figured that hints of Haku's feminine features (having to point out to Naruto 'actually I'm a boy') was there to discreetly allude to potential homosexuality between him and Zabusa (not to claim that all homosexuals are feminine, of course). For kids watching the show, this allusion would probably escape them, but older fans are left to muse. Cleverly done, I'd say, to create an interesting touch to their relationship.
Kishimoto is not afraid of wandering into homosexual love/desire although such sexual feelings are often somewhat obscured. Surely most can see the double meaning of Orochimaru's (also a very effeminate character) desire for Sasuke's body?
Although homosexuality has been less a taboo in Japanese culture than it has been throughout the Western world (and still is, sadly), Kishimoto does seem to be more hesitant about portraying homosexual love as openly as heterosexual love, but there are many pretty convincing examples of it in the series. You don't have to look hard.