Spam box feature introduced by CPanel is considered as a piece of junk, due to the fact that it increases more support. It’s too advanced tool for ordinary people, even advanced users don't understand it and cause some troubles on their emails.
This option allows hiding Spam Box feature in Spam Asssasin, but doesn’t disable the feature. If your clients already enable spam box, it’s still working.
Note: you still able to see the ‘Spam Box’ status by viewing its source code, there is a HTML comment tag display the status.