The dev for the core said there are 64-bit pointers in the code for sound emulation, but they are not used. He's against changing it right now because it would screw save-state backwards compatibility so he's waiting for a bigger reason to change the state code. It is open source, so I was planning on removing them and seeing what happens.
I think there's still plenty of 32-bit Windows users in the community.
@smozoma - heres a link to the issue on GitHub - https://github.com/ekeeke/Genesis-Plus-GX/issues/311