If a certificate has been issued for a domain, and that domain doesn't show up in the certificate transparency logs, that's not something I'd cheer for: that issuer could just as well hand out certificates for your domain to others without you ever knowing about it.

Conversely, if a domain shows up in the CT logs, then there have been certificates issued for those domains, even if there exists a wildcard certificate that is valid for that domain. If that happens, check your settings, because there's probably something requesting certificates you're not aware of.