This might be a limit on the number of mailboxes as this is a tenant with 3000 users? but this here in the Maester script....
$sharedMailboxes = Get-MtExo -Request EXOMailbox -ErrorAction Stop | Where-Object { $_.RecipientTypeDetails -eq 'SharedMailbox' }
Does not retrieve any shared mailboxes, whereas Get-ExoMailbox -RecipientTypeDetails SharedMailbox does