Nintendo must be rolling in the dough, laughing maniacally over the success of their biggest gimmick to date. A genius move to keep quantity below the demand to make them more scarce, which in turn only drives the demand up even more.
If you haven't noticed, the only amiibo's people can find easily are of the common characters. The ones that have a lot of their own games already. People are mostly afraid of the less common characters being discontinued. It's pretty much guaranteed that Nintendo will keep a stock of Mario, Link, Donkey Kong, Fox, Kirby, etc amiibo's, because they're still making games that will likely utilize amiibo usage, so nobody's in a real rush to get those. However, the other characters that don't star in any games run the risk of having no future use, which might lead to Nintendo to stop producing those amiibo's. And if that happens, those specific amiibo's will skyrocket in price. At least that seems to be the mindest of everyone else.
Personally, I think they'll continue to make them until the demand dies out. As long as people are whining and complaining about how hard it is to get them, they'll keep making them in small batches to ride out the demand for as long as they can.
When amiibo's were first announced, everyone was skeptical, there were way too many characters, and $13 seemed like a lot to spend per figure. Hundreds of dollars would need to be spent to obtain all the amiibo's for every character in Smash 4. Although only a handful might have future use with other games. So they sold them in low quantities to test the waters. Then rumors of discontinued amiibo's arose. Nintendo merely took advantage of those rumors and it's been successful so far.