Ironically, Microsoft is in a position to gain rather than lose from web apps these days. The reason is that many apps are developed for mobile first, and getting them into the Windows app store is hard if developer has to spend a lot of time porting. But if the app is HTML/JS, that's a lot easier.

Conversely, Apple benefits the most from native apps, because their development stack is so different from everything else, and yet they are big enough in mobile that everybody has to target them anyway.