The Canaanites, Amorites, etc, were a particularly wicked people that God had been patient with (see Genesis 15:16).

Instead of destroying them with a natural or other disaster, God decided to make an example of them in the judgment being inflicted on them by His people with the iron sword.

This pointed forward typologically to the judgment and mercy that God's New Covenant people would inflict on the whole Earth by carrying out the Great Commission with the Sword of the Spirit, which is the Word of God.

We all deserve death, having sinned in Adam or also by actual transgression. Another reason why God would have wanted the children to be killed was to show forth the completeness of the judgment and overthrow of these desperately wicked nations (pointing to the complete overthrow of the Earth by the spread of the Gospel) and so that Amorites, etc, growing up among the Israelites would not be a snare to God's people.

Thankfully God's people in the New Covenant are not called upon to carry out such a task.

Sadly young children and babies die in God's providence in this sinful and cursed world all the time, in various ways. I leave the ultimate destiny of particular babies and children with God.