I'd be fine with Yooka wearing something. What you pointed out about the connection to the transformations makes sense. I haven't considered that. I guess that's why I liked them a lot more than the transformations in Donkey Kong 64.
Also, remember PlayTonic is trying to stretch the abilities of a chameleon and a bat. Laylee can use sonic waves as an attack. I could see Yooka turning invisible. (Actually, I couldn't see him at all. That's kind of the point.) Espio is a chameleon from the Sonic series (so he wears gloves and shoes), and he can turn invisible in Sonic Heroes. Yooka could totally do the same.