Before I even clicked on this story I thought "well, wouldn't that prevent issues from the game's reliance on a physical book?" Sure enough, that's the reasoning. So this makes total sense.
Ideally, each and every GameStop would inspect the books upon trade-in and make sure to keep one book allocated for each game in stock. But, what's more likely: that actually happening, or people accidentally being sold a game they can't finish and the sh*t storm that would follow?
If people want to sell their game (and book!), since there is no 3DS used-game blocking, there's always eBay!