The real problem came when they shipped the Switch with no virtual console at all. It's obviously easy to run NES and SNES games on even the cheapest modern hardware, so there's no excuse for not letting consumers own and play their games on any Nintendo console.
And maybe they just don't think it's worth spending time on shipping their old games, that it wouldn't be profitable? That would be fair enough, but they are spending time - they just released a whole batch of NES / SNES games to push their online subscription service. Of course, you don't get them just by owning them before - you have to buy them again.
It would have been easy to get and keep the good will of long-time loyal fans with a persistent and growing platform of their classic titles, but Nintendo opted for short-term investments instead of long-term in this case.