The unique art style = bad sales arguement really isn't that strong.
Windwaker was released on the gamecube, which sold significantly less then the N64 and the Wii which is a large reason why WindWakers sales, which are still impressive (4.6m) doesn't match with Twilight princess or ocarina of time . However it still sold more then Majora's Mask.
Skyward Sword (like Majora's Mask) was released right at the end of the generation and so the interest in it was far more muted.
Anecdotally I do know of some people who would steer away from a toon zelda but the franchise is carried by a hugel loyal fanbase who are very much open minded. If anything would hurt the new entries sales, it will be the team producing a game which doesn't actually look interesting.