You are correct it has to do with the footprint of imprevious surfaces. If you use standard wood or trex surface you will need a shoreland permit. No waiver, No variance, just a permit. If you use a product like this for your surface then we consider it pervious and you would not need a permit.
http://www.thruflowpanel.com/about.asp
We do not consider 1/4 inch spacing of deck boards to be enough to be pervious. There are 2 reasons for this. The first is frankly that we do not have the time and resources to get dragged into the middle of a debate on how mauch spacing between boards is enough. The second is that some day the deck will be redone... quite possibly by a new owner that isn't aware of the need to maintain some minimum spacing. There is no was that DES could keep track of those types of projects and enforce the required spacing. It would lead to compliance issues at some point down the road.