A few years ago, I read about a dad who'd been playing a Zelda game with his young daughter (3-year-old, too young to read), and he'd been changing Link's pronouns on the fly so it became a story about a brave young girl instead of a brave young boy. He eventually wrote a patch to modify the gender-specific descriptions (as well as pronouns) within the game. It's described in this blog post (it looks like if you read down in the comments, someone else wrote a wrapper to make applying the patch easier).

I don't know if there's something similar out there for other Zelda games, but would something like this be helpful, or counterproductive?

(FWIW, when I was a kid I loved Legend of Zelda: Link's Awakening on the Gameboy. The Gameboy character design is pretty darn androgynous - there's only a small number of pixels to work with - and the game let you select your character's own name, so I played the entire game with the firm headcanon that my character was a girl and it was just that everyone in the game world kept mistaking her for a boy.)