Let structure emerge organically. When it's imposed from the start, you prematurely constrain what may emerge and artificially compress the nuanced relationships between ideas.
Nature has no outline, but imagination has.
— William Blake
The main premise is there though — notes are short, they usually contain one idea, even if I can't name it yet (this also leads to interesting note titles, like spreadsheets might be a wrong model, or understanding requires effort). Notes are interlinked through direct links, and automatic backlinks (via
muninn cli tooling). If I have a bunch of notes which seem related in some way, I create index note to collect them together, enforcing a specific point of view. Single note can be in multiple different indexes that way (connections are usually better than taxonomies).