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.
I set up /--.pdf to start with. I find that for my yearly document amount, there is no value in adding more than one level of hierarchy. File browser search tools are easier than more hierarchy for the last bit.
I think I will switch my default path to be <correspondent>/filename.pdf (with filename as above). I think organizing by correspondent will give a more meaningful sorting for "manual" access than sorting by year.
For files which are strongly tied to a date, as documents in Paperless pretty much always are, I like to have a YYYY-MM-DD (ISO-8601) format date as the first element. This gives a nice chronological sorting.
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.