If the wildcard SSL option is missing in DirectAdmin's Let's Encrypt SSL Certificates interface, you probably have the dns_ttl set to 0 when it should be set to 1 to use this feature. Check with the following command via SSH as the root user:
/usr/local/directadmin/directadmin c | grep dns_ttl
If so, run the following command to fix this:
/usr/local/directadmin/directadmin set dns_ttl 1 restart
Now, you will see a checkbox option "Wildcard" next to the "Common Name" under the "Free & Automatic Certificate from Let's Encrypt" tab.