I have been using scrivener as my note taking app. It’s actually made for writers and for researchers to make their work (books, essays) but as a note taker it’s very versatile.
I have Scrivener, but I've been using iA Writer much more for note taking. It has wiki links, decent-ish support for x-callback-url automation, and a dead simple filesystem layout that lets me write custom scripts for note mangling when I need to.
https://www.literatureandlatte.com/