Switching to Logseq made me give up on J.D for my notes themselves. I’m building a new (simple AC.ID) index just for my files (which have lost a lot of importance over the last 5–10 years) and plan to leverage Logseq’s page and block properties to reference J.D numbers in my notes (only where applicable, probably in the form a custom property along the lines of johnny.decialmal:: 11.03 or something like that.)
A while back I had a go at J.D notes in NotePlan, though (which, in a way, might be more similar to Obsidian at least, as far as I know!, in the sense that links are links and tags are tags (which is not the case in Logseq)), see AC.ID for notes and files.