From time to time people on the Symantec Connect Forums ask about processing hidden mailboxes. There are all sorts of reasons why you might hide a mailbox in Microsoft Exchange, but the downside of hiding the mailbox is that by default Enterprise Vault won't archive it.
If you have the ability to look at the nice Enterprise Vault Mailbox Archiving Reports, introduced in Enterprise Vault 10.0.2, then you will see things like this:

The good news is that there is a registry key that can be deployed to each Enterprise Vault server, and it will then mean that the mailbox archiving task will process those hidden mailboxes. The registry key is:
HKEY_LOCAL_MACHINE \ Software \ KVS \ Enterprise Vault \ Agents
Name: ProcessHiddenMailboxes
Type: DWORD
Value: 1
I'm not sure why this isn't enabled by default, to be honest. I mean I can't think of a reason why you wouldn't want the archiving task to archive these mailboxes, but, just remember, it's not enabled by default. Once it has been enabled if you then run the mailbox archiving task, or wait until the next scheduled run, the archiving report will show this:

Reference: