Whoo... I still haven't figured out my ideal system for Godot yet but I can describe what I've been doing, which has worked fairly well.
I generally have three main folders, Scenes, Scripts, and Resources. I further split folders by concept or 'functionality'. If I had a 3D tree called "Aspen" then I'd probably have an "Aspen" folder in each of my scenes, scripts, and resources folders.
For resources I usually split things between Materials, Sprites, and so forth so I would have an "Aspen" folder in each relevant folder.
For actual code / script structuring I generally have the main 3 categories, Singletons, Classes, and Scenes.
"Scenes" obviously contain all the scripts for my scenes (each in their own sub-folder, or category if there are several). For example, if I have a couple player scenes that are used for different gameplay scenarios then I would have a folder "Player" with all of these in that folder. Singletons contain global data storage or systems that must run constantly regardless of state. For example, I generally have a thread manager that assigns threads and reports when processing is done, etc. My "Classes" are any standalone scripts that inherit from a Reference. So tools, effectively. I'm currently working on a game with procedural generation so the concept of a "Chunk" would be its own class that I can create / destroy.
Generally if something can 'stand on its own' it gets its own folder. If it relies on something else then it will be in the folder of the bigger piece it relies on.
That's just how I do it. It can get to be a lot of folders at times but finding things is pretty intuitive.