You bring up a good point, one I intentionally left out of my initial article. Nintendo never said the NES Classic Mini was to be mass produced. That is rumor and people misunderstanding what was happening. I do think they missed an opportunity to at least do a larger run later, based on the demand. I understand they did do at least one more run of the plug and play prior to discontinuing it completely but that also was quite insufficient for demand.
I agree, stores should have a strict one unit per customer policy. They have no problem doing this during Black Friday sales - why is something that they will know will be in high demand such as these things any different?
I have heard of various stores allowing employees to purchase units prior to even giving the customer a chance. This screws customers out of a chance to get it, let alone more than one unit each.
I think the reason they didn't produce more probably had to do with them getting ready to mass-produce Switch soon after. We don't know all the details obviously, but there are probably just a select few trusted factories producing their products, and a limited number of new product can be produced by each. They could go out looking for a new one, but that might have come at such an additional financial strain to not be worth the profits from additional NES Classics sold. Considering they are struggling to meet Switch demand (and will almost certainly continue struggling until Christmas when Mario Odyssey is sure to turn Switch into a massively popular gift), I don't want to imagine the situation had they allocated more production to NES Classic at the expense of Switch units for the console launch.
For SNES Classic they had more time to plan and a more accurate assessment of demand based on NES Classic.
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Thanks!