The same thing happens in Magic The Gathering.

There are cards from Alpha/Beta etc. that have an exact same number of printings as other cards worth 10-100x more

The value of short-print cards is to collectors who want the entire set of "Alpha" cards regardless of what the specific card might be.

In the same way, there are probably collectors who want to own the entire collection of NES games or Atari games who would highly value an obscure game with a short print-run.