This is a good question, but it is also a difficult question. It is a hard question because consciousness is a metaphysical rather than a physical concept. What does it even mean to be self-aware? What do we mean when we say “I” want such and such or “I” believe such and such? Is there a physical component of consciousness or is this entirely a non-physical thing? Am “I” merely a neural network in a sea of neurotransmitters? Is a human just a complex animal whose actions are determined by the random interaction of neurons? I believe not. I believe that I have an existence which is joined to my body, but which is not entirely defined by my body or brain. It is this non-physical thing that I am which, at least in part, makes up my consciousness. Here is my view (for what it is worth). I believe that for every non-physical part of what makes me, me, there is a part of the brain that allows my soul–my conscious self to interact with the physical world. Therefore, for most aspects of what makes me, me, there will be a physical component of that which can be observed in the actions of the brain. So… I believe that neuroscientists will convince themselves that they can fully explain consciousness, but that this will be an illusion. There will be determinists and naturalists who will tell you that they can fully explain consciousness, but they will be wrong by a long shot.
You ask what if this happened? My answer is that it will not. We have a spiritual aspect that science cannot explore. Therefore, it is not necessary to ask your question what the impact would be on the idea of soul or spirit. The answer is that it will have none. Or possibly, the impact will be to show what an amazing God-experiencing machine the brain actually is.
Your second question requires me to speculate on the purposes of God. This is questionable territory to delve into. I think you should ask God. But you cannot, so I will give my own little explanation. I cannot tell you why God does what he does, but I can describe what I see to be the pattern. God, for whatever reason, has chosen to use physical processes and the natural laws he created to do things in the universe. God could have simply made stars, galaxies and planets. But, instead, he chose to create a universe with laws that naturally produces galaxies, stars and planets. He could have simply created all the millions of species that have ever lived by simply calling them into existence–ex nihilo as you say. But he did not. He could have simply made Adam and Eve out of stones as John the Baptist said. And who knows, maybe he did. I am open to the idea that the first two humans were simply made out of nothing. But there is reason, based on the evidence, to believe that God used the natural process we call evolution. Why? I do not know, but that is what God appears to do most of the time. Maybe it is kind of like a “free will” of nature. God only intervenes somewhat rarely in the evolution of physical things. I am convinced that God created life from non-life through a supernatural event. Maybe he intervened in evolution similarly. I am not sure, but God seems to prefer to use natural processes to work in this world, and that applies to humans as well. He lets us choose what we will do, generally, without intervening directly.
I hope this helps.