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Unless you want to argue that "Sheik" is the hypothetical character that Zelda's disguise is representing but doesn't truly exist, Sheik is female. Every representation of Sheik clearly is Zelda in disguise, so "Sheik" independent from her is never a real thing.
If you want to get all gender-politics about it, Zelda is pretending to be male (nothing indicates magic in this case) as means to an end, not identifying as male. Sheik is still female.