Two issues. First, I'm not sure why the large number of spontaneously aborted embryos has any impact on what embryos are. If you look at the vast expanse of human history, it wasn't uncommon for around half of children, once born, to die before their first year of life. Many societies turned a blind eye to, or even condoned, exposure and other forms of infanticide and even today, the practice is often easy enough to hide because so many infants normally die at birth or immediately afterward. But even then, people from those societies have expressed that infanticide was wrong and, like abortion, it was often practiced in secret and not discussed.
Secondly, many if not most of those spontaneously aborted embryos are so genetically damaged that they (A) could arguably fail the genetic test of being "human" and (B) lack any potential to ever mature beyond a short number of cell divisions so they have no future, which is the seems to be the key to granting personhood everywhere else (e.g., we deny personhood to the brain dead because they have no future recovery).
I don't normally deal with "souls" because no one can objectively show me when a person does or doesn't have one. But I wouldn't find it difficult to beleive that God can tell the difference between a fertilized egg with a future and one without them and if God is troubled by so many fertilized eggs never making it very far, He could easily know when to withhold a soul, just as He can tell the difference between a white blood cell and a baby or a human and an animal and give a soul to one and not the other.
Ensoulment necessarily occurs at individuation which is characterized by nutrition and growth.
See Aristotle/Aquinas on: