Remember that Amiibo are compatible with an increasing number of games. When you buy the Ganondorf Amiibo, you aren't paying $10 for hard mode in Twilight Princess, you're paying $10 for a collectable figure, hard mode in Twilight Princess, a costume in Mario Maker, a costume in Yoshi Yarn, a thing in Smash, a thing in Hyrule Warriors, and whatever else they want to use this amiibo for in future games.
You might not care about all of those features, but that's Nintendo's approach with Amiibo currently. You buy one and can use it in multiple games for all sorts of things.
Couldn't Nintendo theoretically make even more money by putting out these Amiibo features as digital DLC for people who aren't interested in buying Amiibo (or aren't able to track down rare ones)?
And then they can make money on them again when they buy the digital Amiibo DLC for a separate game, or when they finally decide to plunk down some cash on a physical Amiibo.
By actually giving people these options, the "deal" you get with the physical Amiibo might become a little more apparent.
Of course, this is assuming people are okay with these features being DLC in the first place.