É exatamente onde ele pertence. A partir da página WoW64 da Wikipédia:
The operating system uses the %SystemRoot%\system32 directory for its 64-bit library and executable files. This is done for backward compatibility reasons, as many legacy applications are hardcoded to use that path. When executing 32-bit applications, WoW64 transparently redirects 32-bit DLLs to %SystemRoot%\SysWOW64, which contains 32-bit libraries and executables. 32-bit applications are generally not aware that they are running on a 64-bit operating system. 32-bit applications can access %SystemRoot%\System32 through the pseudo directory %SystemRoot%\sysnative.