Yes, they're discouraging Win32 use overall (even in the x86/x64 space). But that does not mean you can't build native apps (ie non .NET) for WOA - you can use C/C++ out of the box. You are just bound to use MetroUI and WinRT as your primary APIs - both of which are native subsystems.

Steven Sinofsky: http://blogs.msdn.com/b/b8/archive/2012/02/09/building-windo...