Notes in an application are just semi-structured databases. There is the structure of how they are saved, how they relate, but also the data they contain. Apps could offer ways to quer notes by certain constrains, like any other database, but also tools to parse the content into a generic data-structure and then have views to work on them manual or programatic. Keyword for this would be DOM and structured editing.
Usually a document has an internal structure to some degree, like header and body, different paragraphs, sentences and blocks, etc. For some welldefinend formats like there is the DOM (socument object model), but this is something limited to specific formats and purpose. Why not give people thenability ro parae data as they which and then have tools working on it manuel or programatic?
Personally I use some ancient outliner for notes which has a very open scripting-support. It's really nasty garbage and quite limited. But it gives me a tree which is kind of a database and the ability to run scripts over the whole tree and manipulate individual notes.
I use this to import documents or whole folders, break it into pieces, transform the tree by hand or with a script and then export the document again. This is very handy, especially the ability to explore the structure and change by hand when neccessary. For notes this is helpful because I can mass-change them, add properties, change content as I wish and so on.
Though, this is also quite limited because at the end its just an outline with a text-view, not more UI. And alls automation must be written by myself. A proper community could biold new tools, views, parsers, exporters and other automations. But for some reason, automation is hardly used in this space. Emacs org-mode is the only working in that area. But well, it's, emacs..