In this particular case (assuming you're talking about what Twisted posted about), I'd say it has more to do with retailers offering less and less shelf space to Nintendo. Since Nintendo's already committed to making an assload of these amiibos by committing to NFC support for a game like Smash Bros. with a million and a half playable characters, they need to reconcile that with retail shelf space that is becoming more scarce.
Cutting costs and limited retail space have to be what is driving them to heavily promote eShop sales as of late, for consoles without much internal storage space mind you.
If I were Nintendo I would have already started heavily investing in an online store for the US and Canadian market. Like a cross between Nintendo World Store and Nintendo UK's online store. Because
this is bullshit.