The different sizes are really an intersection of ensuring the minimum amount of clearance around the mic to provide optimum wind protection, and ensuring that you have maximum flexibility in terms of distance for mic placement. The smaller windscreens simply let you place those shorter microphones (which are typically not supercardiod) closer to your sound source. You won't have as much close-miking flexibility with a larger windscreen than the microphone calls for. Obviously, this can effect your ambient (meaning environmental, not electrical) signal-to-noise ratio.
Windscreens do have some effect on the frequency spectrum of your recordings, but using a larger than necessary windscreen shouldn't cause anything beyond that effect. Just the previously mentioned placement issue.