Joplin is my choice too. I deplore the complicated codebase, unfortunately. I would have made the changes to get better linking, at least in a personal fork, but I could not find the time to commit myself to it.
[1] https://discourse.joplinapp.org/t/quick-links-plugin/14214
[2] https://discourse.joplinapp.org/t/automatic-backlinks-with-m...