Think about it - Link wears a skirt, could have a long ponytail under that green hood, and Zelda just doesn't see Link in that way. Also, Link's voice acting is almost always androgynous (seriously,its almost impossible to tell Link's grunts apart from Lightning's voice...), and I'm pretty sure that they never refer to Link as a "he" in the Ocarina of Time
timeline (I could be remembering it wrong here...), but instead refer to Link as "child" whenever a pronoun would be more appropriate.
Besides, wouldn't that make a sweet reveal at some point? Eat crow Samus, Link beat you to the "first female videogame protagonist" title by a few years!
So, what do you all think? Is Link a girl?