Hierarchy vs. emergent structures through links between notes
The tool Obsidian makes it very easy to create links between notes. The graphical mode in Obsidian also displays only those links that the user in the text explicitly created.
Niklas Luhmann also linked his notes to each other. But that wasn't the only way he brought structure to his note box. Luhmann organized the notes and devised a system especially for this. He could insert further notes between two notes, even whole subhierarchies of notes.
It was important to him to jump between topics and thus find surprising associations or thematic links. But it was at least as vital for him to put his notes in good order. In this way, he built up arguments, documented "trains of thought," and critically reviewed them repeatedly.
In German, "Train of Thoughts" is also called "Gedankengang," which means "walk of thoughts." These trains of thought are not just arbitrary paths through a network of notes but well-considered and repeatedly revised steps to test and present an idea.
This way of dealing with trains of thought is fundamental to me. That's why I'm working with the "Tools4Zettelkasten" on a system that enables simple networking and structure building via sequence and hierarchy of notes.