In a statement to Wired, Nintendo commented on the seeming lack of restocking for some Amiibo characters, confirming that some 'less popular' figures will not se a second run of production:
We will aim for certain amiibo to always be available. These will be for our most popular characters like Mario and Link. Due to shelf space constraints, other figures likely will not return to the market once they have sold through their initial shipment.
If you want a character that isn't so popular, you might want to go out and get one now, otherwise you may find yourself forced to pay exorbitant prices on eBay.