Using Obsidian for JD Index

I would really like to know how others are using an Obsidian vault for their index notes, using the method 1 of JD where there is a note for each id.

Ideally a tree structure with clickable notes would be available in the graph view in obsidian.

My note 00.01 in each system is my list of areas and categories. It sits in a folder which I have brilliantly labeled <__JD Card File> (to sit on top of the hierarchy. Each ID gets a note labeled, e.g. <14.03 Zoom Backgrounds>. In the note I use a tag to denote physical location, and in some cases I may include some keyword terms or cross references (per the JD Workshop) to aid.

I am still transferring lots of legacy stuff into my systems, and it is getting big - right now close to 400 ID’s are in use (in two separate systems).
each ID gets a separate note in

Does this system leave a hierarchical tree structure, a single overview view like in method 2 where a single file is used, that can be looked at in a glance, to click through directly to an individually stored note?

So what I mean is something like the merging of method 1 and 2, where each ID has its own note but also there exists a note in a hierarchical structure that is clickable through to every other note?