So you're seeing the Information Store, the Public Folder Store and the Exchange Mailboxes, and if you select the last of those three you can't view the the mailboxes which your trying to backup? Certainly you should be able to view that information, so I don't know why you wouldn't be able to.
BE can essentially handle backing up Exchange after you're deleted an account, however the problem you're seeing is with the "mailbox backup" not the "Exchange backup". It's a subtle difference, but while the Exchange backup which includes the Information Store and Public Folder Store does various clever things, the mailbox backup basically just connects to each mailbox individually, reads through the e-mails, and backs up each and every one of them, therefore allowing you restore an individual e-mail rather than the entire Information Store. Since it is trying to open the mailbox, when it gets to those mailboxes which have been deleted from the system, it is no longer able to login, and therefore it receives an error.
Hope that makes sense.