I have used the Joplin webdav synchronization but I wanted to test with the Joplin cloud server (installed on a VPS I own)
- What should be my prefered setup ? Webdav or Joplin server (why ?)
- Is it possible to automatically frequently backup my data in case there is a failure with my VPS (as flat files for example) ?
Depends on what your needs are. If you want/need the extra features provided by Joplin Server (multiple users w/ administration, share/publishing, increased sync performance) then Joplin Server sounds ideal. Otherwise if you just want to maintain a simple WebDAV that you can use for other purposes than just Joplin then just stick with that.
Honestly I would just install the Simple Backup plugin on your local machines and configure them appropriately for the use of that client (i.e. I maintain more backups on my primary machines than I do on a dying Windows laptop but still have one there).
It produces JEX files which contain all your data and if you somehow lost literally everything else you can just set up a new sync target and use the JEX to restore everything.