Interesting that you have so few vaults. I have dozens of them, each for a different project, or for different aspects of the same project. The way folders work in Obsidian is quite bad, when I am creating a new note it insists in putting it into the top folder instead of in the folder where I am currently in, so I prefer to keep it flat. I am just using the default setup and cannot be bothered much with plugins. There is no proper API documentation either.