You say this as if this is the first time Nintendo's been out of touch.
Even by Nintendo standards the shipment of the NES Classic is beyond incompetent. It's one thing for Nintendo to be overly cautious on how they make their online in their games because they worry about pedo's attacking children but to completely under ship something that had so much hype is just criminal.
It almost begs the question on why even make such a thing in the first place if they weren't even expecting it to perform that well? They would have been better of just putting these games on a Wii U disc and calling that game the NES Classic and it probably would have sold the same thing to the hardcore still on the Wii U, making Nintendo more money since it would have cost less to make if they were expecting low sales.
You know I almost wonder if Nintendo intentionally undershipped the thing because after they announced the system and saw all the hype they started to worry if the NES Classic became too successful it would completely kill the Virtual Console. A lot of people were talking about how much of a good deal the NES Classic was because you get 30 games for $60, which is basically $2 per game while the individual games would cost you $5 each on the Virtual Console. If all these people buying the NES Classic were to suddenly by the Switch and see the same NES games they got on the Classic are $5 each on the Virtual Console, they'll be less likely to buy them and just start waiting for more NES Classics to be released. And then of course people are going to be expecting SNES Classic and N64 Classics to come out as well which would make them less likely to buy these games as well in Nintendo's eyes.
So yeah, knowing Nintendo I wouldn't be surprised if something like this might have happened. They removed NES games from Animal Crossing games after the Gamecube version for this exact reason so it wouldn't surprised me if not wanting people to expect these good bundle deals for classic Nintendo game is part of their reasoning. They want people who want retro Nintendo games to buy their own hardware and buy each game individually at higher prices on the Virtual Console and expect that as the only way to get these games outside of these rare once in a blue moon deals like the NES Classic.