Some general, unordered thoughts related to your questions:
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The good thing with digital note-taking systems is that you actually don’t have to care at all about folder hierarchies. I mean, in the end it all depends on your working habits and specific purposes - but a major advantage of digital systems is that you are not forced any longer to spend lots of time thinking about where to put your information, how to name it etc. A note called “Dopamine” can just exist anywhere in your folder structure - doesn’t matter as long as you link to it from within the right place. So, as long as there is a more general topic “Neurotransmitters”, just put a link to your other note and each time you think about Neurotransmitters you can easily jump to your “Dopamine” note.
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If I understand you correctly, your main purpose, however, is to have an overview from time to time: which notes do you already have on a topic, what links from where to where, etc. Sure, you can create folder or name structures for that - but after all my experience I won’t recommend this. It already pre-structures your thinking about how things should connect and behave to each other, thus making it difficult to find new, rather unexpected connections. The better way, in my view, is to use one (or several, or all…) of the following methods:
- Use tagging: If you tag all your single notes that represent a certain neurotransmitter with
#neurotransmitter(or even nested tags like#neurotransmitter_examples), a single click on or search for this tag shows you a list of all notes you have already collected about specific neurotransmitters. - Use MOCs (or whatever you want to call it): That is, establish a basic overview note called for example “Neurotransmitters: Index” or “Neurotransmitters: MOC” and use that note only for collecting different topics and subtopics, by linking directly to the respective notes - you can rearrange your (sub)topics any time, thus reflecting your evolving work on a broader research topic (without thereby breaking any links). Search for “MOCs” in this forum, you will find a bunch of nice ideas how to arrange your information - for example this thread. You can rearrange the idea to your own needs and working habits, but the general idea behind these discussions is exactly the question how to combine hierarchy with flexibility.
- Use tagging: If you tag all your single notes that represent a certain neurotransmitter with
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Luhmann’s naming conventions were especially necessary in a time where all those digital possibilities haven’t existed yet. But in the end his workflow was a kind of combination of having index cards (where he started a topic, put some “table of contents” and registered any new note within that index), source cards (where he put his bibliographical sources) and single, “atomic” notes. One possibility for him was to take an index card about a specific topic - and that index card told him all the information he had already collected about that broader topic and where to find the respective notes in his physical zettelkasten. Another possibility he often made use of: he just opened his zettelkasten, took any random note and explored its content and its linkings (backwards and forwards). His naming habits (combination of letters and numbers) always told him a) where to find that note and b) how it related to the other notes. As I said, we don’t need this anymore today. But there are many people who still like this kind of naming their zettelkasten notes, for various reasons. A short overview of his working system is for example described here (but there are many interesting articles about that).
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The good thing about giving your note files just numeric titles (for example automatically created date-time-stamps) is that you don’t have to care about what the main point of your note is. Just create a note, let it be named automatically (in obsidian, for example, by the zettelkasten plugin) and start typing. There have already been a couple of discussions about the pros and cons of giving “real” names vs. numeric names here in the forum (or a combination of both) - at the moment, of course, real names should at least be part of your file titles as obsidian to date is not able yet to show the headings (instead of file titles) in its file list, which makes it also difficult to open a note with the quick switcher or to link to other note titles. Yet, I think this feature will probably be implemented in the future…