The core principle of Luhmann’s way to manage his notes was a combination of selective tagging, manual links between notes and a sequence of short notes and arbitrary branching („diversification“) of note sequences (see also described in this post).
To my best knowledge, there are hardly any (or even none?) tools that facilitate this workflow, except for the Zettelkasten. Please add your comments, if you know tools, or have built your own workflow that imitates Luhmann’s Zettelkasten-technique.
If you like, you can download the slides of my talk here: Introduction to Luhmanns Zettelkasten-Thinking (PDF-slides).