Even if the sections are physically separated, shared ventilation systems still carry smoke from room to room. Trying to segregate smoking in a restaurant is like trying to have a non-chlorinated section in a chlorinated pool. They are designed to remove the odor of smoke, but do not remove all of the disease-causing agents. Tobacco smoke contains many odorless chemicals and gases. Just because you cannot see or smell smoke does not mean you are not at risk.
Ventilation is an expensive and inefficient means of dealing with secondhand smoke.
Since the average level of measurable tar in American restaurants is currently 202 micrograms per cubic meter, ventilation effectiveness would have to be increased 270-fold to reach that level. This is technologically impractical and expensive. The EPA estimates it costs one dollar per square foot per year just to double ventilation performance. Prohibiting smoking costs nothing, and completely eliminates the health hazards caused by secondhand smoke. Smoke-free restaurant ordinances are essentially neutral in their effect on restaurant sales.