Will Windows 11 stop open source app support for Windows?

I doubt it anytime soon. WSL w/ GUI support is still new and just adds an extra later of complexity. Deploying to Windows is already a PITA and open-source projects already targeting Windows would have to change their build processes. Until WSL apps can be seamlessly integrated and managed like a standard Windows app I doubt open-source project are going to switch away from Windows desktop apps.

In some cases it may. It depends on the app but mostly it depends on the app developer and how they perceive their target market.

A big attraction with Windows has always been consistency and backward compatibility. Apps developed under Win95 still run with little or no changes.

A big issue with Linux has always been the lack of same.

I don't think Win11 and the subsystem for Linux really changes that.

The simplest reason, a bit of a weird answer but you can glean from it all the reasons why:

Typical user wants to use Excel, Chrome & Word which all dont use the linux subsystem.