Before I became more knowledgable in my faith, my husband and I underwent an in-vitro procedure. Two embryos were conceived. I miscarried them both within a week. Did those two babies have souls? It would give me much solace to know that they might be in heaven.
All living things have souls, and all human beings have spiritual, rational souls made in the image and likeness of God. However morally problematic the means of conception, if a human being is conceived then that person has a spiritual, rational soul. So, yes, your children do indeed have human souls. As for their eternal destiny, they share the same hope for heaven that the Church considers that we may have for all unbaptized children:
As regards children who have died without baptism, the Church can only entrust them to the mercy of God, as she does in her funeral rites for them. Indeed, the great mercy of God who desires that all men should be saved, and Jesus’ tenderness toward children which caused him to say: “Let the children come to me, do not hinder them,” allow us to hope that there is a way of salvation for children who have died without baptism. All the more urgent is the Church’s call not to prevent little children coming to Christ through the gift of holy baptism (CCC 1261).