The APP_BASE_URL has to be the one which you are using to connect to the server, so in your case https://joplin.yadda.familyds.net. Did you take a look at this guide?
About your cert question: The nginx server needs to be configured with the cert of your subdomain, however the server on which joplin is running does not need anything, as it only uses http.
If none of the above helps, maybe provide your docker-compose.yml for further help.