when you ad on a domain in cpanel you can access the domain by adondomain.com or adondomain.maindomain.com ...is that considered duplicate content and hurt your search engine ranking?
no because search engines will not access your domain such way. search engine will have the main domain in their index and would not have any clue as to whether it is an addon domain or a single domain on its own hosting
If search engines find a link to ur sub domain adondomain.maindomain.com anywhere in the web, there is a chance to index. So in cpanel, you can set redirection. Redirect adondomain.maindomain.com to adondomain.com. It will fix your problem without any doubt. I have observed this in BlueHost.