That's actually a fairly common cpanel setup. I've never understood exactly why cpanel set's up an addon domain also as a subdomain, but it does. You can also access your addon domains as a subfolder of your main domain. (i.e. 1s.com/2nd.com/)
cpanel is extremely popular so there are literally thousands and thousands of sites setup like this. You are unlikely to have any issues unless you have links pointing to the subdomain versions.