Now, the hall effect sensor may "jitter" around the voltage point where a counter IC may register multiple "pulses" on each pass of the magnet.
Does the counter Dual 16 Bit SN74lv8154 Counter already have some form of "de-noising"?
How big of a unit are you talking? I'm thinking the reason optical sensors are used is because holes have no weight, unlike a magnet. Like Mike said, this seems more like a mass airflow sensor rather than a wind speed sensor.
I use a hall effect sensor instead of a reed sensor to measure my gas ( heating not car ) usage.It's not a sensor that's connected to an analog input but one with a cutoff potentiometer on that is connected to a digital pin.