I agree with you that, for a digital note archive / zettelkasten, it’s best to realize note sequences (chains of thought) via actual links, and not via Folgezettel-style IDs. The latter have issues (such as the problem of decreasing proximity with increasing note archive size, or the lack of multi-parent hierarchies).
Ideally, we’d be able to use link types (as discussed previously e.g. here and here) to describe the nature of a link. That way, we could clearly specify that a particular link points to the next / previous note in a note sequence (e.g. via link types followed by or follows, respectively).
The software could also style links with particular link type(s) in a certain way. For example, in my app, I’ve boldened the arrows/edges matching the currently selected link type(s). Here’s an example with mock-up notes:
