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Some apps are still done this way, e.g. transmission the BitTorrent client, but also ALL self-hosted Web apps. Sure it might feel a bit much to install containers on your phone "just" for that, or having to go through REST API despite being on the same actual device, but still it provides a TON of app.
Anyway, yes I agree that it is often a better model. Still a lot of apps, e.g. Blender, Inkscape, etc do provide a CLI interface. So one can both use them with a GUI or without. It's not decoupled like transmission but arguably it covers most needs.
yeah there are a handful of apps that follow this model, it would be nice if it was the standard way to do things. In fact, this could even be handled by the GUI toolkit itself since native apps have to rely on it to build the user interface. The toolkit could just automatically generate a JSON API based on that for example.