I don’t have much of a homeserver, its more of an experiment - but I have Fedora IoT as hypervisor OS running a Open Media Vault guest and another Fedora IoT VM for container services.
I’m a big fan of Fedora’s Ostree setup, and have used Silverblue on the desktop for a while now, so IoT makes a lot of sense for me.
Joplin could be an option. It can sync either off a cloud drive like Dropbox, or to a server. There is a Joplin cloud which is pretty inexpensive, or you can self host. Joplin can do encryption locally (E2E) before syncing.
Joplin does abstract away the notes files, but its all stored as markdown and the export will give you your notes in a nice human readable folder+file structure.
JabRef with some kind of cloud file sharing or sync? You don’t get a reference manager with a server component here, but maybe it could work. You don’t edit the bibtex file that often, so conflicts should be minimal.