My understanding of the best way to do this has been evolving rapidly. Probably still at the unsettled stage with multiple competing evolved forms before one wins out. There are a few drivers, but the change has come principally because of the success of a few discoveries. Discoveries to me even if not to others.
The original idea, derived I believe from zettelkasten.de is of using single atomic notes as a similacrum of Luhmann's cards. Further propagated by Ahrens and his acolytes. With fancy unique numbers for notes. The unique numbers made linking easier. All the digital solutions, Zettlr etc (I think, I haven't checked) use markdown; I'm not entirely sure why they would do this since the logic of Luhmann's cards would be pure .txt files, and multiple tiny files is not a markdown concept. As BigChungus pointed out on the Obsidian Discord, Luhmann's actual numbering system fits perfectly with the way outliners work. And bullets are a pressure to keep the note short which aids atomicity.
Roam took the outliner idea, added links, backlinks and a graph and went overboard on the idea of a daily note. Like the main outliners, Roam is a cloud database.
Obsidian (I'm not considering programs I have no interest in) sidestepped into plain markdown files, a daily note template, links/backlinks/graphs. Local not cloud. Files, shareable with other programs, not database. But with much of the initial impetus from zettelkasteners and roam observers and escapees, the emphasis was on very atomic notes/files. A tendency exacerbated by block envy and not reversed by block emulation.
I followed this for a while, albeit with small extensions, but dissonance was always present.
A potentially immense number of files always presented management difficulties for other programs - and in Obsidian itself. Multiple folders and files made organisation hard. Advice would be given to mitigate this by using tags, links, search, MOCs. Or the graph, though I have the idea that it's used by a much smaller percentage of Obsidianites than it was in the early days. Daily Notes offered their own organisation. Plugins added further options. It worked, but never seemed intuitive. The text of an atomic thought took so little of a page, always tempting expansion.
My thinking started to move on. I was aware of markdown headers, and even used them a little, but only really thought about them by frustration with managing a MSS copmprised of many, separately written sections. When I realised the potential of long-form markdown files everything turned on its head. Instead of managing small files, it was a question of navigating a single long file. And this was essentially much simpler.
I then started to consider how to work with mindmaps and outliners (can't remember exactly why I started down that path - presumably triggered by using them to deal with a recalcitrant MSS). And then discovered OPML and the easy switching between mindmaps, outliners (inc Workflowy kanban) and a longform markdown file. It was a new world.
Then I moved back to research and notes and asked myself the same question: why tiny-form rather than long-form? As I thought about it, I realised that it would all be easier to manage in long-form. I had nothing tying me to tiny-form - I'd switched from YAML and YAML tags very early, I had everything inline. I was mostly writing, so didn't take it any further initially. But with Obsidian's recent ability to restructure by simply using the outline and folds, I have started to switch in. Anything I do is easy enough to change or reverse but it makes life easier and more intuitive for me. Within file search etc becomes more useful. I can easily switch vaults to outliners or mindmaps. And I don't actually lose anything.
