In Japan, Monster Hunter sales were including Download code/cards and retail sales, but not sales from the eShop. So Download codes are looked at more as a retail sale than a digital sale directly from the eShop.
Nintendo will include download codes as part of their overall sales, of course (but since it's a bundle, they might release two sets of different data for WW at some point. Sales with and without WW HD in the box). But they don't seem to count as digital eShop sales. At least not on the 3DS.