Weird, but not a WTF.
WOW64, short for "Windows-32-on-Windows-64," is responsible for providing two levels of support for 32-bit legacy applications.First, the system files in Windows x64 Edition are not present on just the Windows\System32 folder, but split into two folders to separate the 32-bit applications from the 64-bit applications. The WOW64 subsystem intercepts calls from a 32-bit legacy application and redirects it to the Windows\SysWow64 folder; see Figure 1. If the call is from a 64-bit application, then the call is routed to the Windows\System32 folder and does not involve the WOW64. What's notable here is that Microsoft has retained the name System32 for the folder, which hosts the 64-bit system files. Figure 2, a snapshot from a system running Windows Server 2003 x64 Edition, highlights the classification of the Program Files folder into Program Files, which stores 64-bit applications and Program Files(x86), which stores 32-bit legacy applications.
Second, the WOW64 subsystem also provides redirection at the Registry level; see Figure 3. If the call is from a 32-bit application, then the call to access the HKLM\Software registry hive is intercepted by the WOW64 subsystem and redirected to the HKLM\Software\Wow6432Node. If the call is from a 64-bit application, then it is routed to the HKLM\ Software node. Figure 4, the Registry from a system running Windows 2003 Server x64 Edition, shows the Wow6432Node.
Although the compatibility has been achieved with respect to 32-bit applications, the same is not true regarding device drivers. The 64-bit edition requires 64-bit native drivers for all devices that are part of the system.
From http://www.ddj.com/184405994
Its there for backwards compatability. Don't want to break all those (misbehaving) applications that have hard-coded a path to the SYSTEM32 directory:
Andreas Magnusson: I don't quite understand; it's (some of) the 32-bit apps that hardcode "system32", don't they want the 32-bit binaries?Raymond Chen: It turns out they usually don't! A 32-bit program that builds the path "C:\Windows\System32\control.exe" probably wants the 64-bit control panel, for example.