https://dendron.so has markdown and latex support (disclaimer, I'm the author). its an open source, markdown-based note taking app that works with markdown notes on your file system. also supports backlinks, hierarchies, tagging, and more. its built as a plugin for vscode so you also have access to vim keybindings and anything else you might need with vscode extensions

Coming from an academic background where I need to reference theorems and equations frequently, I've found pandoc and madoko closest to usable. But plain LaTeX (with the help of macros) turns out to be more convenient.