So for the provisioning question, create a provisioning group and position it above all others and call it something like Suspended and tell it to automatically enable users

Being suspended means they won't have anything archived, but their mailbox will get the hidden message telling them webapp url's and such, or you could go one further and enable them all and then jut disable, it's similar to a suspended state but only an admin can enable them

For the provisioning you could add individual users, or an OU or you could create a DL and target the DL
The you can simply add the users via the DL through AD and not have to worry about adding or removing users through the VAC

As for the indexing, how are you determine the number of items in the archive and how many they have indexed? Also what version of EV are we talking about as EV10 uses a new indexing engine and troubleshooting is vastly different

If you are on EV10, was this user created on EV9? If so have you converted heir index to be 64bit?
Typically what happens is when items are archived, they are added to be journalarchive table where it tracks whether the item has been backed up and whether it's been indexed

Those counts depending on a threshold number may trigger events in the VAC to let you know of a backlog, things that might stall indexing would be slow retrieval through storage, the server being busy or the storage service beig stopped

Something that might stop indexing altogether is the indexing service shut down or in read only mode or the index itself is failed, but if it was failed a search would return zero items and display an error
You could if you really wanted to, just rebuild the index, but first I would just try an update of the index to see if it kick starts the process

But the importan question is, how are you determining the numbers?