What makes you believe that? When Microsoft refers to Desktop apps as "legacy apps" and metro apps as "modern apps" it doesn't help, I know. But Sinofsky has said he understands the importance of a dedicated mouse+keyboard interface for office, design, and development apps.
And I couldn't imagine Visual Studio running under the current version of Metro. So I think they're waiting until Metro is seriously improved years down the line to remove the Desktop, or they're serious about the Desktop being permanent and are just postponing major updates on it to get the buzz around Metro.
If the Desktop is permanent, I imagine Desktop apps will have some type of appx model and ClickOnce installation, and will use the WinRT API, so Desktop apps will be windowed Metro apps, and the nomenclature "modern" vs "legacy" is correct in either case.