The first question I have is whether or not your subdomains are all owned by the same user.
Secondly, what directory are you in when you run the ls command?
By default, on DreamHost, all you domains (and subdomains) are placed in named directories directly under you user directory.
In other words, if you log into the shell at yourdomain.tld, you will find yourself in your “user” directory (/home//username). In this directory you should see your “domain” and “subdomain” directories (/home/username/yourdomain.tld, /home/username/sudomain.yourdomain.tld, etc.)