In a recent interview Aonuma explained Link’s more androgynous appearance was in order for more people to be able to relate to him. This has been the goal in most of the series outside of Twilight Princess.
“Back during the Ocarina of Time days, I wanted Link to be gender neutral. I wanted the player to think ‘Maybe Link is a boy or a girl.’ If you saw Link as a guy, he’d have more of a feminine touch. Or vice versa, if you related to Link as a girl, it was with more of a masculine aspect. I really wanted the designer to encompass more of a gender-neutral figure. So I’ve always thought that for either female or male players, I wanted them to be able to relate to Link.”
“During the development of Twilight Princess, I went a different route and created a version of Link that was more masculine. But after Twilight Princess I went back to the drawing board and decided Link should be a more gender-neutral character. Hence I created the version of Link that you see in Breath of the Wild. As far as gender goes, Link is definitely a male, but I wanted to create a character where anybody would be able to relate to the character.”
“So that’s why I think the rumor went around that Link could be a female. Because maybe the users were able to relate in that way.”