When running e-receipts, records that have no email addresses listed are not pulling into an exceptions query after the merge is completed. Records that do not have an email will not show a letter in preview and are not being marked as either Acknowledged or Receipted at end of run. There is no notification that the process was not completed for this type of record.
As specified on page 198 of the Mail Guide, this is caused by the option chosen on the eReceipts tab: Specify what happens if no email meets this criteria: Remove record from run
Because the record is being completely removed from the mailing, it is not included in the exception query.