I think you can add a Ghibli "tone" and maybe some flourishes while still keeping the core animation CG, like I'm thinking some kind of hybrid of 90% CG look but just a dash of 10% Ghibi/Japanese anime styling.
But full blown anime/hand drawn style I think is out of the question. It would limit the box office potential way too much, unfortunately there's just too many people outside of Japan/Asia who refuse to see a hand drawn animated movie in this day and age.
Zelda can be a billion dollar movie franchise of its own, and I think Nintendo is going to make damn sure they do everything they can to get it there, choosing an animation/art style that cuts your box office potential off at the knees is not happening.
Beyond that also I think Nintendo will definitely want a Smash Brothers movie one day, and to make that doable Link/Zelda probably have to be CG like Mario and Luigi are.