If someone says "The sky has been purple for the past three years" the right response is "I think someone would have noticed". There are however reasonable responses to this. For example, "No one noticed because we're all brains in vats! And I have proof! Look here."

Similarly, I think Wednesday is right to say "Someone would have noticed that God didn't exist." it's just that in this case Aunt Alicorn has a really good response: "Lots of very smart people have noticed, you just haven't met any since you've spent your whole life around people who chose to believe in God or never knew any other option. We've tried to tell your people this but you all get pretty upset when we try. Here is our evidence, x, y, z."

Obviously if you keep repeating "Someone would have noticed." after the dissenter has shown that indeed, people have noticed and that there is good reason for why more people haven't noticed then you're doing it wrong.