Are you certain about this?
From what I could understand from Wiki, taxation applies to all incomes of lords/dukes, not only from their share, which makes much sense, otherwise all would be easily obstructed in the way you describe (the way it is currently on).
The region tax is split among all the knights of the region. The lord sets a Lord's Share that comes out of each knight's income.
The Duke sets a Duke's Share that comes out of each lord's total income. (This comes off the *total* of what a lord gets, which includes the lord's income from his own estate, if he has it.)
The realm sets a Realm Share that comes out of each Duke's income, which includes any income he gets from his estate (if he has one), his Lord's Share (if he is a lord) and from the Duke's Share taken from each of his lords.
If the duke has no estate, is not a lord, and sets the Duke's Share to 0, then there is nothing for the realm to take as a Realm Share. Of course the duke won't get any income.