Well... the burning of gasoline (or alcohol) also emits water vapor together with the CO2. And, for a given amount of energy generated, the burning of gasoline emits more water vapor than the burning of hydrogen.
The burning of hydrogen generates far more energy than gasoline, so less of it is needed to generate the same amount of energy, and so less water vapor is produced.
So, if this problem does not happens with normal cars, it also wont happen with hydrogen fueled cars.