Hi,
I recently started migrating my JDEX away from a single file into multiple notes. But I use vimwiki and its functionality so I have a “full wiki toolset” for keeping and managing it. So far this has been quite good. And one side effect of it is that I keep more notes directly at IDs. So I would say that a supportive technology helps a lot here (be it Bear or vimwiki or orgmode or whatever).
However most of my notetaking is done on paper. 
I’m one of these people always carrying around a small notebook and something to write.