I’m just reading How to Take Smart Notes, and that is my only knowledge of Zettlekasten, beyond trying Zettlr so far. It definitely seems like every software implementation of Zettlekasten that I’ve seen so far completely misses the idea of his linking convention, by only including a date-based UUID, which doesn’t link conceptually at all.
(Zettlr uses UUIDs, but you can also include names in the links, and the links recognize and use the UUID and ignore the text.)
(I haven’t tried http://zettelkasten.danielluedecke.de/en/ because it requires Java to install. But Smart Notes recommends it. I’m wondering if it has a better implementation that does have those kinds of strand links. Do you know?)
This doesn’t address the numbering you are talking about, but it could be a good supplement. Have you read up on the concept of Maps of Content by nickmilo? On the process of making MOCs