I saw a similar situation occur when a friend set up his internet accounts on his Mac and subsequently turned on mail synching in iCloud. As near as we could figure out the two different sets of ccounts were not recognized as duplicates — probably because he had capitalized the account address on one device and not on the other. The fix was to make the capitalization the same and the second set of accounts disappeared. Normally I use myy desktop computer as the account setup "master" and the setup on my iPhone and iPad follows suit through the iCloud synch.
Deleting an internet account on your iPad does not delete the account on the host server, it just prevents your iPad from accessing the data on the account host server until the account is re-established on the iPad. Normally messages, contacts, etc. associated with the account are stored on the account host server. You can verify the data is on the account host server by logging on through the account's web interface.
