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.