Hi @gigatux,
in regard to the article: I use a mix of links and search (ripgrep & Helm-rg) to find relevant notes. Occasionally, I also use Devonthink to find related notes. No issues whatsoever, despite more than 2000 notes in three languages (approaching two years of usage).
I write fleeting notes on paper and later add them directly to the relevant note - following here Ahrens 2017, “How to make smart notes”. The book had considerable impact on the way I take notes, although I already used plain text files and unique identifiers when I wrote my Phd years ago. To this system I only add new notes for information that I want to remember in 2-20 years time. I have external folders for meetings, lectures, and projects (with files sometimes in .org format, sometimes not).
I love the freedom Emacs gives me to set up a system how I want it. And if macOS ever becomes an unfeasible choice, I can easily move my notes to a different OS. I don’t see myself ever leaving this again (but I might update to v2 soon :).
Cheers!