See also: Is there any way to write a WinRt (Metro) app that will also work on Windows 7 and Vista?
I am trying to understand how to target both Windows 8 on Arm and
The definitive answer is out now. There will be a desktop, but you will not be able to install desktop apps. "WOA does not support running, emulating, or porting existing x86/64 desktop apps." All apps will come from the store and will have to abide by the Metro style app guidelines.
The only desktop apps appear to be Office (which seems to ship with the OS) and built-in apps like the control panel, Explorer, IE, etc. Everything else will be a new Metro-style app written against the Windows Runtime.
See this Building Windows 8 blog post for details.