In the context of what OP is asking this is not true. DNS zones aren't enumerable - the only way to reliably get the complete contents of the zone is to have the SOA server approve a zone transfer and send the zone file to you. You can ask if a record in that zone exists but as a random user you can't say "hand over all records in this zone". I'd imagine that tools like Cloudflare that need this kind of functionality perform a dictionary search since they get 90% of records when importing a domain but always seem to miss inconspicuously-named ones.
> Even if it were not, the message you pasted says outright that they scan the entire IP space, so they could be hitting your server's IP without having a clue there is a subdomain serving your stuff from it.
This is likely what's happening. If the bot isn't using SNI or sending a host header then they probably found the server by IP. The fact that there's a heretofore unknown DNS record pointing to it is of no consequence. *EDIT: Or the Cert Transparency log as others have mentioned, though this isn't DNS per se. I learn something new every day :o)