The computer learns over time, and such a minor mod as the deckplate/ISR shouldn't cause it to do anything out of the ordinary. Basically it will slowly adjust its settings to take advantage of the extra air, just as it did when the supercharger was installed.
As for the dust, you may have to clean the filter more often but as long as you keep up with your maintenance it shouldn't hurt anything. Just make sure you don't over oil the K&N as this may affect the MAF sensor.