If this were to be supported then perhaps nested vaults should be made a first-class feature in the app.
For example, clicking a button in the file browser (New vault alongside New folder with a globe icon or safe icon perhaps) to create a new named vault, then creating files and folders underneath it. Notes inside a vault can only reference notes within the same vault, while notes in a parent vault can reference down to notes in a child vault. It creates a sense of direction in links. Encryption could be added as a feature on a per-vault basis, so you can right-click the vault name in the sidebar and configure it. Etc.
Vaults then become essentially “named groups of folders” from the app view.
And it keeps app configurations (themes, CSS, plugins, etc) consistent across sets of notes. (although I am currently finding a benefit in having a vault for zettelkasten and one for project management, with the same themes/CSS but different plugins to meet the needs of each – so perhaps workspaces can help out here?)