In theory, 3DS titles are meant to be priced the same for their package and download versions. In theory.
In practice, retailers appear to be pricing the download versions higher than the package versions. Full article.
Don't they get some special freebies with the Digital Download? Still, I found this interesting to discuss. Let the "Nintendo Sucks at Online Services" fest begin.
Edit: From the article about the campaign for the launch of online game sales "Buy the download version of either game, and you'll receive Donkey Kong Original Edition on the 3DS Virtual Console and double the Club Nintendo points, or 40 points per game. Buy both games, and you'll also get an addition 20 Club Nintendo points as a bonus"