Do you mean that using the waterproof housing you reduce the windnoise? Or is the skeleton house/waterproof housing not the same?
The GoPro comes with two housings, the waterproof one and a regular housing with vents.
The waterproof housing is used when you want a tight seal so no water can get in, while the regular housing is used for everyday stuff.
The waterproof housing does reduce wind noise but it also reduces regular/wanted speech. I personally use the waterproof housing all the time since i dont really care about audio, dont want dust and other foreign stuff to get into the housing.