When you hear a hypothesis that is completely new to you, and seems important enough that you want to dismiss it with "but somebody would have noticed!", beware this temptation. If you're hearing it, somebody noticed.
Disclaimer: I do not believe in anything I would expect anyone here to call a "conspiracy theory" or similar. I am not trying to "soften you up" for a future surprise with this post.
Suppose: Wednesday gets to be about eighteen, and goes on a trip to visit her Auntie Alicorn, who has hitherto refrained from bringing up religion around her out of respect for her parents1. During the visit, Sunday rolls around, and Wednesday observes that Alicorn is (a) wearing pants, not a skirt or a dress - unsuitable church attire! and (b) does not appear to be making any move to go to church at all, while (c) not being sick or otherwise having a very good excuse to skip church. Wednesday inquires as to why this is so, fearing she'll find that beloved Auntie has been excommunicated or something (gasp! horror!).
Auntie Alicorn says, "Well, I never told you this because your parents asked me not to when you were a child, but I suppose now it's time you knew. I'm an atheist, and I don't believe God exists, so I don't generally go to church."
2. Ignoring Soothsayers
Wednesday's environment reinforces the idea that God exists relentlessly. Everyone she commonly associates with believes it; people who don't, and insist on telling her, are quickly shepherded out of her life. Because Wednesday is not the protagonist of a fantasy novel, people who are laughed out of public discourse for shouting unpopular, outlandish, silly ideas rarely turn out to have plot significance later: it simply doesn't matter what that weirdo was yelling, because it was wrong and everybody knows it. It was only one person. More than one person would have noticed if something that weird were true. Or maybe it was only six or twelve people. At any rate, it wasn't enough. How many would be enough? Well, uh, more than that.
But even if you airdropped Wednesday into an entire convention center full of atheists, you would find that you cannot outnumber her home team. We have lots of mechanisms for discounting collections of outgroup-people who believe weird things; they're "cultists" or "conspiracy theorists" or maybe just pulling a really overdone joke. There is nothing you can do that makes "God doesn't exist, and virtually everyone I care about is terribly, terribly wrong about something of immense importance" sound like a less weird hypothesis than "these people are silly! Don't they realize that if God didn't exist, somebody would have noticed?"
To Wednesday, even Auntie Alicorn is not "somebody". "Somebody" is "somebody from whom I am already accustomed to learning deep and surprising facts about the world". Maybe not even them.
3. Standing By
Suppose: It's 1964 and you live in Kew Gardens, Queens. You've just gotten back from a nice vacation and when you get back, you find you forgot to stop the newspapers. One of them has a weird headline. While you were gone, a woman was stabbed to death in plain view of several of your neighbors. The paper says thirty-eight people saw it happen and not a one called the police. "But that's weird," you mutter to yourself. "Wouldn't someone have done something?" In this case, you'd have been right; the paper that covered Kitty Genovese exaggerated the extent to which unhelpful neighbors contributed to her death. Someone did do something. But what they didn't do was successfully get law enforcement on the scene in time to save her. Moving people to action is hard. Some have the talent for it, which is why things like protests and grassroots movements happen; but the leaders of those types of things self-select for skill at inspiring others to action. You don't hear about the ones who try it and don't have the necessary mojo. Cops are supposed to be easier to move to action than ordinary folks; but if you sound like you might be wasting their time, or if the way you describe the crime doesn't make it sound like an emergency, they might not turn up for a while.
Events that need someone to act on them do not select for such people. Witnesses to crimes, collectors of useful evidence, holders of interesting little-known knowledge - these are not necessarily the people who have the power to get your attention, and having eyewitness status or handy data or mysterious secrets doesn't give them that power by itself. If that guy who thinks he was abducted by aliens really had been abducted by aliens, would enough about him be different that you'd sit still and listen to his story?
And many people even know this. It's the entire premise of the "Bill Murray story", in which Bill Murray does something outlandish and then says to his witness-slash-victim, "No one will ever believe you." And no one ever will. Bill Murray could do any fool thing he wanted to you, now that this meme exists, and no one would ever believe you.
4. What Are You Going To Do About It?
If something huge and unbelievable happened to you - you're abducted by aliens, you witness a key bit of a huge crime, you find a cryptozoological creature - and you weren't really good at getting attention or collecting allies, what would you do about it? If there are fellow witnesses, and they all think it's unbelievable too, you can't organize a coalition to tell a consistent tale - no one will throw in with you. It'll make them look like conspiracy theorists. If there aren't fellow witnesses, you're in even worse shape, because then even by accumulating sympathetic ears you can't prove to others that they should come forward with their perspectives on the event. If you try to tell people anyway, whatever interest from others you start with will gradually drain away as you stick to your story: "Yeah, yeah, the first time you told me this it was funny, but it's getting really old, why don't we play cards or something instead?" And later, if you keep going: "I told you to shut up. Look, either you're taking this joke way too far or you are literally insane. How am I supposed to believe anything you say now?"
If you push it, your friends think you're a liar, strangers on the street think you're a nutcase, the Internet thinks you're a troll, and you think you're never going to get anyone to talk to you like a person until you pretend you were only fooling, you made it up, it didn't happen... If you have physical evidence, you still need to get people to look at it and let you explain it. If you have fellow witnesses to back you up, you still need to get people to let you introduce them. And if you get your entire explanation out, someone will still say:
"But somebody would have noticed."
1They-who-will-be-Wednesday's-parents have made no such demand, although it seems possible that they will upon Wednesday actually coming to exist (she still doesn't). I am undecided about how to react to it if they do.