(Opinion) Will Flatpak and Snap replace desktop Linux native apps?

Yes, I think so. It's a lot easier to maintain your distro if the maintainers of the project handle everything regarding application packaging.

To me, it feels similar to what's happening on the server side. Server Side, most application handling got replaced with containers, because the dependency management becomes untenable if you're pushing around just a couple of in-house applications. Here you use the distribution to offer a stable platform (container engine, monitoring, storage and such) and then run container on top.

And I think the desktop is on a similar journey for similar reasons, at least for faster moving or more complex applications.

I hope so. The fact that packaging and in essence software distribution has become a distro maintainer's task is really weird and shouldn't be.