The slow sync (both in Syncthing and Joplin), especially when doing the initial synchronisation, is expected in Android 11 and newer. There is no direct filesystem access and everything has to go through FUSE (look up "android fuse" if you're interested in details) which can lead to extremely slow performance, in particular when dealing with large numbers of small files located in a single folder.
When it comes to the notes not showing issue, I've got a feeling that you might have been hit by https://github.com/laurent22/joplin/issues/6517, especially if you tried to perform the Joplin sync while Syncthing was still downloading the data. There's no easy fix for that one, unfortunately. I would suggest to make sure that your Syncthing synchronisation has fully finished first, then uninstall and reinstall Joplin (or just wipe the app data), and only then try to perform the first Joplin sync using the filesystem target. Make sure to keep the phone screen on until the sync has finished completely (which can be done by setting the screen timeout to a very high value in the OS settings or disabling it completely in Developer Options).
Just for reference, you may want to have a look at https://forum.syncthing.net/t/how-to-deal-with-abysmal-i-o-performance-on-android-10/18406 which describes my fight with syncing Joplin files onto Android with Syncthing. In the end, I had to basically reduce note history greatly in order to minimise the total file number, and in addition to that use the workaround described in https://github.com/laurent22/joplin/issues/6517 to finally achieve reliable synchronisation.