There are many things to consider when changing your exhaust system. I recently read a set of awesome posts in here somewhere, and this was covered in great length. Besides the major tuning differences that are made when you start changing things from original design, I don't understand why pod filters wouldn't suck up water from rain or whatever. (Carwash?)
So why is exhaust velocity so important?
The faster an exhaust pulse moves, the better it can scavenge out all of the spent gasses during valve overlap. A fast moving pulse creates a low pressure area behind it. This low pressure area acts as a vacuum and draws along the air behind it. A similar example would be a vehicle traveling at a high rate of speed on a dusty road. There is a low pressure area immediately behind the moving vehicle - dust particles get sucked into this low pressure area causing it to collect on the back of the vehicle. This effect is most noticeable on vans and hatchbacks which tend to create large trailing low pressure areas - giving rise to the numerous "wash me please" messages written in the thickly collected dust on the rear door(s).
The H-Box plays an important role. And the air box keeps the carby from sucking in water droplets. Not sure how much a problem water is for a bike fitted with pods though. But I have enough problems