Very good question. I guess it depends on the software in the controller. For some, it probably won't make a difference, but others have a power profile that is related to cadence (cadence is measured by the rate of pulsing), so the controller will think you're pedalling faster, so will give high power faster if that's what you want. Other controllers might count the pulses and start when they count enough, so you'd get quicker response with more magnets. Maybe there's other reasons, but I can't think of any.