I don't think this can last, because whatever advantage structured text files in a file tree provides over an API will be maximized by some format that is better than a file system.
That might mean leaning into SQLite or some other open format. My own thought is that a graph-like structure of documents will be ultimately more valuable than either a tree-like structure or a database-like structure.
But if a proprietary implementation of whatever usurps structured text in a file-system becomes popular, that company will have significant leverage.
Two advantages I see to files in folders are the ability to browse and the ability to easily read - by both LLMs and humans.
But I also agree that this has limitations. If I were to challenge you and say that Obsidian solves this, or gets close to solving it, what gaps would you say were left unfulfilled?
I am because I'm working on something in this space and your comment touches on my three main ingredients: text files, SQLite, and graphs.