As an owner of a Miata/MX5, I can say that the 6spd felt like a better all around tranny, but the 5spd is used largly in autocrossing due to its gearing ratio. The final gear in both cars is not very far from one another, so in the 5spd in 5th gear you are very close to the gear ratio of the 6spd in 6th gear. I like my 6spd, but if I were to do autocrossing, I would pick the 5spd any day of the week.
Ultimately it could have come down to the cost, which I am sure is more expensive, or Mazda may have not been willing to sell its 6spd.
