This highlights a huge problem with LetsEncrypt and CT logs. Which is that the Internet is a bad place, with bad people looking to take advantage of you. If you use LetsEncrypt for ssl certs (which you should), that hostname gets published to the world, and that server immediately gets pummeled by requests for all sorts of fresh install pages, like wp-admin or phpmyadmin, from attackers.
It's not just Let's Encrypt, right? CT is a requirement for all Certificate Authorities nowadays. You can just look at the certificate of www.google.com and see that it has been published to two CT logs (Google's and Sectigo's)
Why would you care that your hostname on a local only domain is published to the world if it is not reachable from outside? Publicly available hosts are alread published to the world anyway through DNS.
LetsEncrypt doesn't make a difference at all.
I like only getting *.domain for this reason. No expectation of hiding the domain but if they want to figure out where other things are hosted they'll have to guess.
> If you use LetsEncrypt for ssl certs (which you should)
You meant you shouldn't right? Partially exactly for the reasons you stated later in the same sentence.
That may be related, but it's not what happened here. Wildcard-cert and all.