Try running the .appref-ms shortcut via rundll32:
inParams["CommandLine"] = @"rundll32.exe dfshim.dll,ShOpenVerbShortcut ""C:\New App.appref-ms"";
Alternatively, instead of relying on the shortcut path, you can use the application deployment URL (you can see it by opening the .appref-ms file in a text editor):
inParams["CommandLine"] = @"rundll32.exe dfshim.dll,ShOpenVerbApplication http://github-windows.s3.amazonaws.com/GitHub.application";
, Win32_Process.Create .