The reason that these "last" flights are often cannot be held for late connecting passengers is usually a simple logistical one... if there is any substantial delay in arriving at the outstation, then there may well be pilot rest issues that prevent an ontime departure for the following morning's flight back to the hub. So the next morning's departures get delayed, and those passengers miss their connections.

So it is not just simply waiting a half hour for late connecting passengers. It is done when the plane is not going to turn around at its destination or when crew duty/rest issues do not come into the equation.