on my dietpi installation nextcloud is running via diepi installer,
and pairdrop + searxng via docker/portainer.
I can reach nextcloud via https but pairdrop and searxng only via http.
Where do I need to make changes? to the servers themselves or to docker or letsencrypt?
I guess you would need to create a reverse proxy with your web server to allow connection to the container. Depending on your web server, it could be complex.
i do not need to reach all at port 80 im fine with adding a subfolder or use x.x.x.x:3000.
For subfolders, you still need to configure your web server as a reverse proxy. The advantage of a proxy is that it handles SSL processing for you. You do not have to configure each app individually. Take a look at your app/container documentation. Usually, most provide examples of how to configure a reverse proxy.