I just setup Seafile 9.0.4 under Sonoma 14.3 on Seafile CE 11.0.5 but it’s not completely healthy. I’m also seeing problems with SeaDrive under Sonoma and Ventura (that share a login).
The process I went through is very similar to what you describe: I completely uninstalled the previous Seafile 9.0.4 using a utility similar to your own; I renamed the user’s previous Seafile folder (Seafile_bak); restarted Seafile and completed the sign-in process; setup a new Seafile folder as requested; copied back user files and allowed sync; checked results against the web login. I might be advantageous to un-sync all folders prior to un/re-installing the service.
I see the Finder icons but have not checked for them in Open/Save dialogs.
In the Seafile application menu, however, I only see a spinner in the Main window where the Libraries and Shares should be listed. This just happened. I did see them previously.
I hope this helps.