The main target of the Godot Engine are game developers. But Godot's easy workflow and functional UI elements, makes it also a good fit for non-game applications. There are already some out there you may know, like Pixelorama, an Open Source 2D sprite editor.
Like others have said, it's pretty much the same as web development. The logic can live anywhere, so you could build your own app with whatever architecture you want and even use best practices from other fields as inspiration (Like the Redux comment.)
What we're missing is mostly more people actually doing it, having opinions on how best to organize app-like builds. I've built some small apps using it but nothing complicated enough to answer these questions.
But there are some examples that are open source to look at.
https://github.com/LyffLyff/Veles
https://github.com/Mad-Cookies-Studio/mad-productivity
https://github.com/RodZill4/material-maker