What @seazen said is more along the philosophical route, maybe that will give your pensive child more to ponder? You can say along the lines of mommy and I love each other so much that we wanted to have a child as a product of that love. To continue life. I don’t know exactly how to put it, but I was always told that children are a persons’ immortality. And, it is not that he has to be just like you or his mom, but that he was created as his own unique being to be part of the world and part of your family. That experiencing life is a gift, and you wanted to have children so they could also experience that gift.
Each of us becomes ourselves through the many experiences we go through, that helps shape our personalities and our perspectives on life. So, he is who he is, because of what he has gone through, and he will continue to change and grow. Maybe point out to him how much more he knows now than when he was 5, that life continues like that, we learn more and more, and it only gets more interesting.
I’m rambling. I guess once you get started, you can change direction depending on his follow up questions.
It also comes to mind, ours is not to question why, I never really question why do I exist? Why am I me? Why do we exist in the universe? I feel no need to answer these why questions for myself. I just think this is how it is.