There's been two places in the SMN quests where we find SMN Soul Stones. The first would be from Tristan, and those are the Soul Stones that the Immortal Flames are using to train Summoners. The second is the Node in the Lvl 70 SMN quest. In order to create the Egi of Sari, it needed to be hooked up to several Soul Stones. Those were somehow "eaten" by Principa for safekeeping in the event more Soul Stones were needed.

For the oldest Soul Stones we've yet come across, there's honestly a lot of SMN Soul Stones. It's just that the job has a lot of other prerequisites that keep it rare (being around for the defeat of a primal without being tempered mainly). What I would not be surprised to learn is if the Allagans with all their aetherchemistry figured out how to mass produce soul stones and made lots of them very quickly. Summoners weren't around for that long after all. It would explain why enough Soul Stones survived to the preset day for there to be multiple copies still around. We've probably got more Summoner Soul Stones then White Mage, Black Mage or Scholor Soul Stones at the moment.