Ok, I re-read your original post and I think I was confused on what you were asking. Are you saying that a simple get-mailbox includes the inactive ones as well when it shouldn't?
I'm not seeing that.
Try this to make it go faster
Download , install and use the V2 Exo PS Module:
Then run these and see what you get:
This should only list active mailboxes
(Get-EXOMailbox -ResultSize unlimited).count
This should only list active and inactive and be higher than above
(Get-EXOMailbox -ResultSize unlimited -IncludeInactiveMailbox).count
This should list only inactive mailboxes and be the difference:
(Get-EXOMailbox -ResultSize unlimited -InactiveMailboxOnly).count
If I am not understanding question correctly, let me know!