Thing is, even when web apps are essentially used as desktop app replacement (Electron etc), all the complexity discussed here is still there.
As far as looking OS-native, this is (unfortunately) increasingly less relevant as OSes themselves drop desktop UX consistency even internally. But that aside, Qt is still around and is a very mature framework for "near native" UI, and then there's Avalonia and others. Even Gtk is surprisingly decent on Windows these days. Although I'm not sure what this all has to do with the original subject, since web apps most certainly don't look native anywhere.
For one, clients (mobile, desktop) are drastically different with all sorts of downstream implications:
- Differing screen size requiring responsive design
- Internet speeds magnitudes different
- Intermittent internet
- Uneven feature support due to different versions of browsers
- Everything needs to be JS at the end of the day
Desktop apps generally don’t have to worry about any of these issues.
Also, desktop GUI frameworks are typically either fragmented (one per OS) or don’t look OS-native.