created emails not showing up in manage accounts

You could check what permissions the other hundreds of accounts have set on their directories/folders. That would give you a clue.
/home/user/mail is 0707 user mail. Contents vary from 0707 to 0750 but are created and permissions set automagically.

Has the account been given a quantity of email accounts in the WHM package to be able to set up accounts?

In WHM you could try using:
Email/Mail Troubleshooter or
Email/Rebuild/Fix Mail Dbs/Boxes

From your question the answers could be many and varied.
HTH