Not to be a conspiracy theorist, but they must know they are losing tons of money with limited quantities selling out so I'm guessing they are either forcing market prices to go up and selling in online markets for gross markups or doing reprints eventually like gamestop has done with xenoblade, the calling, one piece, and probably others I didn't pick up on.
Is it all amiibos that are hard to find or only some? It's likely marketing made bad decisions to start with and then they probably were not prepared to manufacture enough to meet demand. If you ever collected action figures you know it can be a pain to find specific characters simply because there are never an equal number of each figure made. The hero or lead protagonist of a series always gets produced in the greatest quantities so I'd guess Mario figures get at least 25% of a case if not 50% or more. When I worked in a toy store way back in the '90s we'd get cases of Batman: The Animated Series figures. There would be 20 Batman in a case, 2 Robin, and 2 villains. Of course, demand for villains was high because kids wanted someone for Batman to fight and collectors loved the villains too, for value and because the show was great. You'd think they'd be smart enough to produce more villains but they never did. They simply assume if people are going to buy anything they'll buy Batman first so make the most Batman. There would also be full cases of just Batman, typically in a silly outfit like Lightning Strike Batman.
Power Rangers hit the scene at that time too, and they were not prepared at all for demand. Bandai was making the figures I believe and they didn't have enough factories. The figures were junky too so they'd break and people would want replacements leading to even less stock. Over time they expanded and increased production but it took some time. Power Rangers is also a good example of male characters being more widely available than female. I wouldn't really expect that for amiibo but this is the video game industry, and too many fools in marketing still believe most customers prefer male characters. So in Power Rangers you'd get lots of Red Ranger, plenty of Blue and Black, and then maybe one Pink and one Yellow per case.
