I find Roam Research to be the the most zen note-taking app. The database takes a lot of mental overhead away and just allows me to write, and I know I won't have to deal with files and folders at all. You could mount a Logseq graph in a location where it isn't easily accessible to other programs and yourself, and restrict the permissions to read-only expect for the 'Logseq' user, so that you think about the plumbing less often. And the new sync that they're adding will make it all even more zen. Syncing with cloud services or using Syncthing gives me a bit of anxiety over data loss.