Corporate offices purchasing officers have the job of purchasing the items for sale in their store from Nintendo. I know this, because, at one time, I was one. Nintendo is a mainly retail based multinational corporation who does not own the factories that produce their goods. I currently work for one as well, so I understand a bit about how this works. They have many many many deals with many factories to produce a variety of products. If they could not fill the orders the purchasers of other retailers made, I can guess that it is likely Nintendo would not do business with them anymore.
If there was a chip shortage causing a lack of stock, that would be one thing. To my knowledge this isn't the case, but what do I know. Nintendo decides how much stock to produce, agrees to purchase rates for customers based on available stock levels, and it is up to the production facilities to produce enough to meet the agreements.
If a multinational retail giant technology company cannot meet demand, their business is in trouble. It is far more likely that they are producing fewer units to moderate financial risk or control budgets in some way for their company.
Unless I'm wrong, in the case of these units, it was stated that there would be limited supply, but more than NES Classic Mini. That's intentional. Also, Nintendo is controlling who has permission to do pre-orders. All of this is Nintendo. No one, but Nintendo.
