I'm pretty sure they've always been regular people-shaped faeries. It's just an artstyle thing.
or, you know she has (relatively) huge wings that extend deep into the light that obscures the complete bodyIn the OP I addressed the technical limitations being the likely original intent when it comes to the original OoT, but later depictions of Navi and similar fairies make it so the proportions don't really make sense for a tiny human to be in there - the wings in particular are too far out.
![]()
she'd have to be hunched over constantly or something, if she had normal human proportions