Referring to the admin SDK APIs, I don't see anything that would allow me to list the subdomains defined for the google apps domain (via the CPanel in Domain Settings->Domain Names).
Is there any way to collect this information directly? Even the older provisioning API doesn't support any listing of subdomains and/or domain aliases.
There are no domain-specific API calls that allow you to list out secondary domains and domain aliases. However, you can try listing all users (with aliases) and groups (with aliases) in order to see which domains are in use. Technically, this may not be all domains (some may not have any users/groups associated with them yet). But for practical purposes it should serve.
Obviously the performance would be much better if you could perform a single API call and get all domains but there's currently no method for that. This is the only workaround I'm aware of.
