.NET is not going away anytime soon. If anything I feel this further deprecates silverlight. There is no way that MS expects the majority of apps to be written in HTML+JS, it's just an option to make it easy for those used to HTML+JS to write apps on the platform, in the same vein as writing an HTML+JS app for iPhone. Most serious Windows applications are written in C++ for Win32 anyway, VS which is becoming more and more .NET everyday still has heavy roots in COM/Win32. Office integration is still best done in C++. No these apps aren't whats fueling the consumer web but they make big bucks for the vendors who write them, and ensure platform lockin to Windows as MS tries to transition away from their desktop monopoly.

MS is not stupid enough to pull another Vista and make apps that used to work not work. Even if MS were very serious about transitioning everything to HTML+JS you'd be looking at a 10-15 year timeline. The day you see Office written in HTML+JS is the day to start worrying if you're a Win32 / .NET app developer.