it's worth being skeptical whenever someone's argument involves their not being able to comprehend the magnificence of their own creation (it's a form of argument from ignorance).
Not really. Not if they're using a genetic hillclimbing approach with neural networks, mutation, and evolution. Chances are, you'll never have any hope of understanding what evolves in that case. That's normal, and nothing to be skeptical about. And that would be a great way to win Core Wars.