Of course Nintendo limits stock intentionally. This is in their interest for two reasons: 1. they sell out faster (which consequently makes the perceived value of amiibo higher and thus a better product to sell) and 2. they never have to keep amiibo in inventory. Compare this with Skylanders and Disney Infinity figurines, which are abundant and take up store shelf space. There's no telling how many of them are kept in inventory at warehouses. That's money lost as it's doing nothing. Nintendo's amiibo are making money for Nintendo, they're not just sitting there as inventory.
Nintendo wants you to preorder amiibo and buy them as quickly as possible because any other way they'd stay on store shelves with the rest in warehouses, which is money lost for Nintendo. And that's what amiibo is all about: a way for Nintendo to make money. Their strategy has been extremely successful considering how quickly even modestly "rare" amiibo tend to show up on eBay only to be sold at 2x or even 4x the RRP. Essentially amiibo sells on its own, Nintendo doesn't even need to market them that much because the hype takes over for that on its own.
amiibo cards will be another way for Nintendo to make money, though it'll be interesting to see what their strategy is for such cards. They likely don't want to make too many of them as they'd cannibalize sales of the figurines, but on the other hand they're supposedly coming out to "combat" the short supply of amiibo figurines (which is entirely intentional and part of Nintendo's business plan). I wonder if the amiibo cards will instead be bundled with compatible games like AR cards for 3DS.
