That's very odd. Perhaps you could try to use the 'recover username' function to check if the username is indeed connected to one of your e-mail addresses? If it's not connected, you might have to ask yourself if there's any chance at all that maybe you did have a separate e-mail address for Neopets at some point.
If you're 100% sure you've got the right e-mail address & username, I wonder if it might be possible that someone hacked your account and changed the e-mail address associated with it.
You said you were able to see that your account still exists on Neopets; can you see if anything (pet colours/amount of pets/etc.) looks different from when you last played?
Either way, sending another message to Neopets support seems like a good idea; try to include as much information about your account as you can remember. And maybe ask them if they are able to see if one of your e-mail addresses used to be associated with the account, and if there's any chance the e-mail address on the account has been changed in the time that you were unable to log in.