no one will be able to know that any add-on domains, are 'added' to the main/top account domain. in reality CPanel treats add-ons as subdomains of the main domain -> second-domain.com.main-domain.com <- and then handles the redirect automatically...no one will ever see it, and the search engines seem to have no issues either
the real issue is that if you are planning on having a lot of domains? (I have over 30 live domains) you really will want to get a CPanel/WHM (reseller) account or Ensim Pro (now Parallels) either of these will let you set up domains to have their own log-in, and folder structure. this way you will not be looking a ridiculous amount of folders!
think about it...set up say 10 domains...with 9 add-on domains? they will show as folders in your main CPanel public_html folder, ALL mixed in with your main domain's folders, and subdomain folders! very very easy to make a mistake.
as long as you are careful you will be fine...but in the end? I still prefer to have each domain have it's own account.
R-