Wow, i honestly had no idea people are using that many graphs…
To me, the main feature of Logseq is that I don’t have to think where to put anything. I just write in the journal, and tag it. I use it almost as a paper notebook, so there’s private and work stuff, notes about people I met, ideas, research… and I never clean it up 
So it looks super messy, but through tagging (this i do consistently!) I can easily find the relevant information, and crucially: it stops me from procrastinating with (folder/graph/etc) structures.
But of course: whatever works for you.