Personally, I find Luhmann's indexing method to be deeply tied to the physical nature of the index cards he used — a form of clustering information together to aid browsing. I would have my doubts about trying to impose any global order on the notes through their IDs. The moment our notes cease to be tree-like in structure and become a graph (possibly containing cycles), we can no longer have any top-down structure.
However, along the same lines of discussion, there is an ordering in the way we visit notes, creating one (or many) linear narratives throughout. I think this could be very valuable in a Zettelkasten system.
With large pools of notes, it becomes unmanageable to pinpoint the information we're seeking. So we rely instead on forms of fuzzy search to get us within the vicinity: keywords, tags, master pages, or search grammars. However, even this is can sometimes not be enough — I will often find myself relying on note links when I'm not even sure about what I am looking for, that "I know something about X" feeling. Or for mind-wandering. Or when I'm looking for a particular angle.
In the book "How To Take Smart Notes", Sönke Ahren quotes Luhmann "conversing" and being "surprised by" his slip-box. I find this description spot-on: we converse with ourselves by linking thoughts through semantic relationships. This build context around the information and makes the initial entry point less crucial. Sometimes the value is not in the final note but the traversal: how did you get to this piece of information, what it relates to, and what sparked the relationship.
This process feels to me very much like keeping a few stacks of notes, moving up and down as thinking unfolds. On top of Joplin's search functionality, the ability to jump hyperlink backwards and forwards helps somewhat. So does the Graph UI for a bird's-eye view. But I find myself often relying on the Note Tabs plugin to "anchor" thoughts as I move through them, to avoid losing some of that context.
This concept of stacking is executed beautifully in Andy Matuschak working notes. The layout used makes the traversal explicit by piling up notes horizontally as we click links, providing a visual representation of the process of "I was thinking about this, then this, then this...". The preview of links is also a nice complement to "look ahead" without clicking.
I would vouch for some plugin that would allow a similar track record of the notes visited. Some mechanism that would trigger after performing a search and keep records as we click through links, perhaps "branching off" on-demand by using "alt+click", middle-button click, or any other well-established convention. Apologies for the long-winded post, but I thought that the Why might be more valuable than the Hows for this discussion.
I suppose this idea could take many forms in the hands of a great developer/designer: visual stacking like the example above or something as simple as an extension of the idea of "browsing history" in our internet browsers. Code management systems like git solve similar problems in presenting the information, though this is perhaps too much of a conceptual jump.