O Windows de 64 bits não inclui o WOW - mas, de acordo com a Wikipedia, o Wine 64 bits faz isso!
Fonte: link
Backward compatibility in Wine is superior to that of Windows, as newer versions of Windows can force users to upgrade legacy Windows applications. In many cases, Wine can offer better legacy support than newer versions of Windows with "Compatibility Mode". As illustrated by screenshot on the left, Wine can run 16-bit Windows programs on a 64-bit operating system, which uses an x86-64 (64-bit) CPU. 64-bit versions of Microsoft Windows cannot run 16-bit Windows programs
Fonte: link
The Win16 subsystem is available in 32-bit editions of Windows NT, 2000, XP, Server 2003, Vista, Server 2008, 7, and 8. The 64-bit editions of Windows versions that have them, however, do not include the WoW Win16-support subsystem and therefore cannot run Win16 applications, nor do they provide the NTVDM emulator. DOS and 16-bit Windows applications, therefore cannot run in 64-bit versions of Windows without third-party emulation software (e.g. DOSBox) or a virtual machine with either a 32-bit version of Windows, Windows XP Mode, or DOS itself.
Se possível, execute duas VMs - uma com o Windows de 32 bits, uma com o Windows de 64 bits, supondo que você precise especificamente do Windows de 64 bits.