I highly doubt it. If you're talking about bombing a run and seeing which one will go faster, your body passing through the air is more resistance than the base of the snowboard on the snow, and even then effective edge has nothing to do with the surface area of the base.
Effective edge means that when you are carving, for a given board you will have more edge actually contacting the surface of the snow. Theoretically you'll have less weight per inch of edge, and you could turn harder without the edge starting to slide.
So that said, does more effective edge help you ride faster? In a way, yes. By having more edgehold on hardpack, you can ride faster and still remain in control, but that has nothing to do with straight line speed.
Yes I forgot to factor in wind a real life stuff to this! I think if the board with the longer effective did happen to have more surface area you might be able to go a very unnoticeable amount faster, but like poutanen said the wind would negate most of that