@hieuphay -
You are making some interesting points, but there are a couple of issues being conflated. One is whether it makes sense to somehow mark a difference between notes that are concepts and notes that are ideas or arguments. The point of a ZK is ultimately written output, and probably anything you write for other people will be a combination of concepts and arguments, so I can’t see the benefit in separating them structurally.
You also say that structure notes are good from the point of view of the structure note, but not from a graph view. I find the idea of a graph view that can be navigated by clicking appealing, but it is not clear to me that it actually would have any tangible benefit. But even if it does, it would be a benefit that showed itself in a different stage of working with the ZK than the structure note would. I think navigating in a graph would be good for discovering “accidental” connections between ideas. Creating and working with a structure note, on the other hand, is a prelude to writing and putting thoughts in a more structured organization.
To me, one of the benefits of software like org-roam is that it has the potential for looking at a set of notes with different views that might each yield different benefits. You can have many structure notes that organize the same group of atomic notes in different ways to achieve different goals.
Lastly, I can’t imagine that there will be any type of software that could organize a collection of 1000+ notes in a way that wasn’t completely messy. I don’t think any practice should be discarded because it would result in a messy graph view!