There’s a simple logic to this one: Services are available securely depending on what domain they’re under.
We can provide the Panel and WebFTP securely because they all reside under dreamhost.com, which we have a certificate for.
The Mailbox Manager runs on a subdomain of your domain, so we cannot enable HTTPS for it: chances are that no SSL certificate exists for mailboxes.example.com. (Even if one did, we don’t have things set up in such a way that we could install one.)
phpMyAdmin is a special case. It runs on your domain, so it’s available over HTTPS if your domain has secure hosting enabled.