Though this situations with Nintendo, usually also show problems in the distribution inside the retailers.
Like the aformentioned Fire Emblem Fates Special Edition. It had a really short preorder window and was sold out for months. Yet, come day of release, both Best Buy and Amazon put additional stock they got for sale before fullfilling all preorders. Some even with preorders got their orders delayed or cancelled in the meantime.
The recent $99 3DS, some stores got dozens of them while others got 5 or less. Amazon even decided to allow preorders without notice the day before.
The NES mini because of been a hot item, has been the eye of scalpers. So you have people in stores buying any stock they have (1, 5, 10), you have people online using bots to buy 5, 15, or more.
Retailers can do preorders without Nintendo's permission, (random example) by creating a SKU for it, allow people to pay for it and then come release void that and charge it with the real SKU. They can also put limits in stock so to only sell one per person or one per account (online).
But the reality is that some retailers also enjoy this kind of situations. So a person that goes to their store, doesn't end with they they wanted can go and purchase something else, that might even bring a higher proft margin to them. Stores like Wal-Mart, Target, Best Buy they barely make any money on videogames. But if a disgruntled customer went to but a NES mini, was pissed off that it was sold out and noticed a 4KTV (or whatever) on his way out for cheap and even decides to get the store credit card, even if denied; that already brought more money than the lost mini sale.