My production SME server runs SME 9.1, migrated from 9.0, migrated from 8.something, migrated from 7.something, etc., probably going back to 3.something. There's doubtless a lot of cruft in the config database. It's configured with four domains--the primary and three additional domains (one of which is a subdomain on the primary domain).
When I go to the Hostnames and addresses panel, I get a list of "Current list of hostnames for $PRIMARY_DOMAIN", containing a number of aliases for the SME server itself, as well as entries for a number of other machines on my LAN. And that's it. It doesn't show hostnames for any other domain. When I click the "Add hostname" button, I get the screen to create/modify the hostname, and it contains a dropdown for the domain, but the only item in that dropdown is the primary domain. I don't appear to have any way to add, remove, or change a hostname on any other domain.
My test server (also running SME 9.1, but as a clean install with no migration from previous versions) behaves quite differently. When I go to the Hostnames and addresses panel there, I first see the list of hostnames for the primary domain, followed by a list of hostnames for the secondary domain. I can add, remove, and modify those entries independently.
I expect this is somehow related to cruft in the database, but how to track it down?