About missing directories:
Something went wrong at Docker container initialization 
Digging into code, I found that the directories should have been created by https://github.com/mailserver2/mailserver/blob/26c8ab63404198c297a02fe29a9ba9fe81b2fb92/rootfs/usr/local/bin/setup.sh#L807 (to be run once at container first run, see https://github.com/mailserver2/mailserver/blob/26c8ab63404198c297a02fe29a9ba9fe81b2fb92/rootfs/usr/local/bin/run.sh#L139).
You can try the following:
cd /mnt/repo-basedocker-compose -f -s rm mailserver && docker-compose up -d && docker-compose logs --follow mailserver- exit with Ctrl+C when the log start to be very verbose (after “s6-supervise : spawning …” lines)
If you can see a line saying “[INFO] Finished container setup”, then your setup is probably OK.
You can check with docker-compose exec mailserver ls -alR /tmp.
You won’t lose any data, unless you made any other changes than creating /tmp directories, into your container (would be a very bad move, BTW).
About certificates:
The HTTP link between your domain certificate (no prefix) and Nginx is made in /mnt/repo-base/config/nginx/sites-enabled/nextcloud.conf.
You should see lines like this in the “4430 ssl server” section:
ssl_certificate /certs/live/domain.tld/fullchain.pem; ssl_certificate_key /certs/live/domain.tld/privkey.pem;
The SMTP/IMAP link is done by mailserver Docker container, please check in your /mnt/repo-base/docker-compose.yml:
services:
mailserver:
image: mailserver2/mailserver:1.1.16
container_name: mailserver
domainname: ${DOMAIN} # Mail server A/MX/FQDN & reverse PTR = mail.${DOMAIN}.
hostname: mail
...
volumes:
...
- /mnt/repo-base/config/letsencrypt/certstore:/etc/letsencrypt
Maybe container re-creation will put it back on the tracks…