Well last month they dropped more prices on the Nintendo Selects line. And 3DS at least still has new retail games releasing.
I think they should drop more because why would anyone pay $50-$60 for this (or other games that flopped like Paper Mario: Color Splash) when you could just buy a pre-owned physical version for much cheaper? Nintendo won't see any of the money from a used copy but they'll see 100% of the money from an eShop purchase.
Obviously I wouldn't expect them to drop the eShop version of this game to $5 just because one store is selling it for that price, but $50 is too much (and if I remember correctly the $50 version doesn't even come with the Star Fox Guard half of the game, it's an extra $10 for that).