To answer one of your questions... Yes, Cpanel does handle subdomains (3rd level domains).

Technically, you can ping any domain to see if it is alive, however that isn't a true indication of if a subdomain is in use.
It could be that the domain/host is down at the time you ping it, so it would not respond.

On the other hand, whois only works for top level domains.

Your solution would be to use nslookup to actually find the nameserver of that domain, then use nslookup to switch to that nameserver and query for all the cnames.