Why do you think it would be a stupid thing to do, please elaborate...

Because they are losing out on so much potential revenue during the busiest shopping period of the year. 

it's not, they just didn't think it would sell that well just like Wii

Well people can easily buy the amibos on eBay so in all honesty this is not really a planned shortage and in the long run they are only hurting themselves.

How so the people selling them on E-bay didn't get them for free, they still put the expected amount of money into Nintendo's pocket ...

Let's say a person buys one amibo for $30. He then sees that many people are struggling to buy an amiboo and therefore decides to sell it for $40 since even though he wanted the amiboo he didn't want it that much. Only one direct copy would have been bought from Nintendo. Now if the first person ounce again bought the amiboo for $30 from Nintendo but there was no shortage he wouldn't have sold it. Therefore the person who bought the $40 amiboo from Ebay would have bought a $30 amibo from Nintendo and so Nintendo would have gotten $60 not $30.

P.S: Welcome to VGChartz The_Yoda

Would you be willing to lose out one Christmas season to sell better the rest of the year with inflated demand? Again I'll site the Wii, it was hard to come by at least one season yet it did not seem to cost the in sales in the long run, it was in demand for quite some time. Not only that but it was riskier as there were other consoles a consumer could purchase, not the case with either the adapters or the Amiibos so far as I know.

@ Bolded, Thank you Mr. Playstation

I would concede to that being a possible outcome. Would you be willing to entertain the idea that some buyers might pick up a figure or two right away that they would have put off buying while being under the impression that some of the "less popular" figures are a limited run and have been discontinued?  That would get you sells now that although they may occur later they may not as well.

I DON'T CARE JUST MAKE SURE MY GAME HAS A WIDE RANGE INSTEAD OF LIKE FIVE AND NO PITY-PAT!

/rant.

Gamecube Controller Adapter -> Nintendo is hurting them BIG with that shortage.

Amiibos -> too much demand in conjunction with too many characters means trouble.

Kudos to Nintendo PR for making the most out of the Amiibo situation which seem only to be that worse within the US.

In Europe there is no shortage on any of the Amiibo characters. Nintendo should be more worried about having them not presented that well and having less shelf space than Skylanders or Infinity...