That's what outliners are good for. You automatically generate context and proximity when adding/indenting outline items. And we have the thing called hypertext for cross-referencing and navigation. I think Luhmann's zettelkasten is a quite poor concept in comparison, because the cards are small and don't adjust to the size of a topic, so we have to split topics, and we have to take care of identification and referencing the cards ourselves. When translating zettelkasten to digital, then at least we can get rid of some of these limitations, but we still don't have all the advantages of outliners.
In my experience, it is purely a matter of habit whether you write down ideas or thoughts by hand on paper or enter them directly into an outline on the computer. Before I had tools like Ecco or my own CrossLine (https://github.com/rochus-keller/crossline/), I also produced a lot of notes on paper. After a few years of working with these tools, I got rid of paper completely. With CrossLine, I also solved the problem of linking to other documents or emails, so that I can link any information or put it in the necessary context. And it scales well. I have outline files with thousands of notes, minutes, concepts, specifications and the like, everything cross-referenced and full-text searchable. I can still reproduce e.g. meetings or paths to decicions taken ten or more years ago with little effort.