You can write x86 or x64 assembly in a Windows Store app as long as it fully follows the required ABI, you mark the package appropriately for the architecture, and it doesn't import any DLL exports that trigger the WACK tool validation. The Windows 8.0 SDK
includes the x64 assembly macro include file macamd64.inc that makes it possible to create proper x64 ABI assembly modules.
All that said, if you can rewrite the module to use compiler intrinsics instead that is a much better way to go.
Note that the Windows 8.0 SDK does not include the required assembly macros for writing correct ARM ABI assembly, so writing ARM assembly for Windows RT apps isn't supported.