Link notes densely
Every time a note mentions an idea that has its own note, link it. The links are where the thinking compounds: following them surfaces connections you didn't plan.
This only works if notes are small. It also means a note gets more useful over time without being edited, because new notes link to it — those show up under "Links to this note".
Links to notes that don't exist yet are fine — they show as dashed text, like An idea I haven't written up yet, until you write that note.