Presumably the Creator can create new souls, perhaps out of the energy of the destroyed ones, or he has reserves, or has energy to recycle. RJ was reluctant to answer such questions in Q&A, he wanted the cosmology to remain mysterious as it is for the characters, only Rand has something that amounts to a Revelation at the end of the story (he knew "all the secrets", and it's implied knows better than to spread them out).

Shadowspawn would not be extinct the next turning, RJ just implied their souls cannot be reborn as anything else than Shadowspawn after a life as one. So millions of souls are now tainted, possibly not that significant since it's possible they've been tainted since the first turning and just return for a round in each Second/Third Ages.

That could be problematic as Turnings go on. Maybe there's a cleansing of that at some point.

RJ gave that answer for Shadowspawn when asked if Constructs like Green Men and Shadowspawn had souls and if they came from the Soul Pool. He said souls for Nym come from the Soul Pool and are thus just borrowed for a life, and are reborn normally after, but souls for Shadowspawn get tainted and can't be reborn after as anything but Shadowspawn. So the implication is that the Shadow can permanently taint some souls and deprive them of a normal cycle of rebirth and choices etc.

IMO, RJ implied heavily that souls produce the OP thread called Spirit (so the Creator can presumably make new ones and introduce them in the Pattern via the Soul Pool), but it's really just implied.

I suspect destroyed souls are more like "undone" and a new soul can be made out of their raw energy.

I was also suggested in AMOL that souls turned to the Shadow are now in Shai'tan's possession, that the person is technically "dead.

There's the motif for the Shadow that Shai'tan can annihilate free will altogether. Grey Men (who however give their souls willingly, or so it's believed anyway), Turned people, souls used for Shadowspawn, mind-traps. Does it ever get fixed and how, we don't know.

The Encyclopedia might have some answers.

Rj was consistent in Q&A when he decided to give cosmology answers - it's likely he had a lot worked out in his notes about this - but it wasn't a topic he was very keen to give us a lot about.

I suspect it was mostly to make sure he didn't reveal too much and that the confrontation with Shai'tan wouldn't feel anymore like Rand was having some big revelations about the cosmology.

It was also very derivative, for the likely answers it's pretty much a mix of Zoroastrianism, Taoist concepts of harmony, and concepts like Samsara, all simplified. The whole idea of one big confrontation between a warrior-champion vs. the Beast per cycle of the Wheel of Suffering, after which the world is "remade" but not really is borrowed straight from Jainism (from which the Way also came from).