I think 3D is a fine idea! Definitely worth trying in general.

In the context of this thread my mind was mostly on what it takes to make some arbitrary power UI "not dreadful", i.e. easy to understand for newcomers. Since it's a power tool, assume there'll be a learning curve. But the initial experience doesn't intimidate someone to start on that journey of a hundred miles of understanding how to use it with fluency and thereby augmenting themselves.

There have certainly been many intuitive 3D UIs. 3D games devote a lot of attention to being discoverable and friendly to newcomers, and they have a lot of success. However, my impression is that they achieve this success by dint of hard work. It's not clear that 3D makes the problem easier. If anything I'd be more likely to believe it makes it harder.

So if you have a product and are thinking about how to make it more intuitive (as I am), "make it 3D" is probably not the best suggestion. Does that seem reasonable? Let me know if I'm missing something.

I like your codepen. I wonder what it would feel like to use a whole note-taking app or digital garden with this metaphor. Rotate to a particular note until it's in front, then click on it to edit it. Perhaps you should stop moving in 3D while editing.

To give credit where it is due, the codepen is not mine, but from this page: https://r3f.docs.pmnd.rs/getting-started/examples from @react-three/fiber.

My guess, and only a guess, is that 3D is especially (only?) useful for navigation. As in moving around documents, panes, windows, etc.

As for "I wonder what it would feel like to use a whole note-taking app ..." The note taking is in some ways already done pretty well. So my current guess is that it is more the navigation that would benefit.

I don't really have answers, but I often feel like I live in 'flatland' these days.