I doubt that, unless they up production (I have a feeling they will make more, particularly around MP4 release). People have wanted a Metroid Amiibo for a very long time, even without considering the really great new 3DS game. Of all the new Amiibo announced at E3, this sold out the absolute fastest - even faster than the new Zelda four. Add in that we all know Metroid Prime 4 will almost certainly use them in some manner. This is going to be a really popular pack and I doubt it heads to clearance.
Plus the Metroid amiibo is squishy. How cool is that?