Through C++/CX for the .NET side of things. I'm entirely sure it's all possible yet, but I'm working on that side of it ATM and it seems to be going fairly smoothly... Is that not going to work?
C++/CX is C++ with some extensions to support accessing the new Windows Runtime (WinRT); it is primarily syntactic sugar for COM support. C++/CX produces native code as WinRT is a native code framework. You cannot mix managed and native code in a C++/CX project, so you cannot even combine it with C++/CLI. Using C++/CX -- like using C++ -- gives you a 100% native binary.
C++/CLI looks the same as C++/CX because Microsoft basically lifted the syntax. C++/CLI would let you produce managed code, but it isn't C++ -- it's a managed language, so at that point you may as well just be using C#. There is no point to ever using C++/CLI unless you are writing an interop library to expose a native API to managed code or the other way around.
Yeah, you're not. WinRT isn't .NET, it's not related to the CLR or managed code at all. Furthermore, you can't even use DirectInput for Metro apps in WinRT.
I might not be using the proper term here and may actually be referring to WInRT. But it all looks very similar to .NET to me... I wouldn't want to use a wrapper here either, I would want to interface directly with the library where at all possible for the clearest picture of what's going on.
It sounds like all of your plans are based around an assumption of compatibility, when in fact the technologies you're all talking about are quite incompatible at varying levels. You should probably revisit your plan by determining what platform you want to target or what language you want to use and then doing some research into what is possible with that platform -- MSDN is an excellent resource, you should start there.