No, it doesn't matter what the Emulator supports it could support 18 cores and it still doesn't matter, the Operating System MUST support Multiple processors other wise a "64 bit" emulator is just a useless peice of trash wasting valuable HDD space. If you can't find a windows OS that supports Multiple processors and programs executed in long mode (which IS the definition of 64bit) suchas XP Pro or Vista(Blegh) cheap then don't even bother downloading a 64 bit program because it won't work or look for a linux distro and compile the source for the emulator you want IF it supports Linux.
Any way it's not the Program that supports multi processors anyway it's just programmed to support running in long mode. As i said it's the OS nothing else. if the kernel can't recognise more than one processor (or 64 bit) it simply isn't going to work.
EDIT:
Wait, I just realized something your a Mupen64 developer nmn, you should know this it's fairly basic DynaRec isn't going to do jack squat for pseudo 64 bit environments or dual core because it always comes down to the operating systems limitations. If it doesn't support graphics rendering with out a specialized plugin it's not going to work is it? as it was DOS couldn't do anything remotely graphical without OpenGL then Microsoft hopped on the bandwagon with GDI and then DirectX years afterwards, however dual core and 64 bit environments fall under a different category it MUST be in the Kernel's source code otherwise it will never be possible to run a 64 bit application with out serious coding and an expanse knowledge of ASM (which simply isn't worth the effort)
EDIT2:
If you haven't already please look up registers it's vital information to a programmer.