What sense does it make for monsters to actually exist in the Scooby-Doo universe, when the whole point is that monsters are always people in costumes? Because that's precisely what makes dressing up as a monster such an effective disguise.
I thought that Scooby-Doo meeting Batman in one of his movies was a strange combination until I realized: Batman is exactly the type of person that the gang usual is up against, since he dresses as a monster and uses all sorts of gadgetry specifically with the intent to terrify. He just uses it for good instead of evil. If they'd gotten the chance to unmask him, they'd have been shocked to discover it was the least likely suspect of all... Old Man Wayne!
Something I thought about when reading the Evil Counterpart trope page and noticed the Mystery Inc entry. After reading that, I thought about what other similarities members of Mystery Inc had with their predecessors when I thought of what makes Ricky into Shaggy's Evil Counterpart more subtly. More obviously, whereas Shaggy's still best pals with Scooby, Ricky and Pericles were pretty much barely on speaking terms, to the point of hating each other's guts for the longest time. The subtle one lies in the fact that Shaggy is pretty much a hippy, or at least looks and acts like one to a point. What's a good evil counterpart for a hippy? How about the CEO of a massive soulless corporation that defiantly doesn't care at all about the environment.
Stop and think for a second of the situation from the heroes' points of view. They're alone and completely defenseless as they are running through the dark being chased by a shrieking psychopath wearing a mask.
The episode "A Clue for Scooby-Doo". Underwater in a sunken ship, they find a dead man in a diving suit with his oxygen hose cut, so he presumably suffocated down there completely alone. What's worse, the Villain of the Week was trying to do the same thing with Fred, Velma and Daphne, and as they still had a link to their oxygen tanks, had they remained trapped, they would have lasted quite a while before dying.
It should be noted that the dead man was actually the villain who had faked his death the whole time.
Not only that, but the instances where members of the gang are kidnapped and confined in different areas ("Go Away Ghost Ship", "A Gaggle Of Galloping Ghosts" "Which Witch is Which?", etc.). Sure, the bad guys don't do anything to them, but how do we know if they'd have released our heroes at any future point?
Episodes like "A Gaggle of Galloping Ghosts" or "Hassle in the Castle" where the villain is a criminal wanted in several states. It's never mentioned what they're wanted for, and in any case, a man who's on the run from numerous state authorities might not hesitate to off a few meddling kids who were coming too close to blowing his cover.
In "Bedlam in the Big Top", Daphne is put under a trance by a ghost clown. The next time we see her, she's wearing a tiny costume dress. Erm... Maybe it's a good thing she couldn't remember any of what happened while she was under that trance.
Even moreso when you remember that the same villain showed a gleeful willingness to feed Shaggy to a lion or watch Scooby plummet to his would-be demise from a high wire. Would he have given a thought to sparing Daphne's modesty, or worse, once he had her in his power?
In "To Switch a Witch", a friend of the gang is being persecuted by a group of townsfolk for the belief that she is a witch. They were explicitly going to torture her to make her confess. Fortunately, Shaggy and Scooby take the brunt of it, and come out okay, being Made of Iron. But the young lady who was their original target? These people weren't the "Monster" of the week, and seem to get off scot-free for their willingness to harm an innocent girl. Including elected officials like the town's mayor.
The movies did address that, just in time for that not to be the case.
This is discussed in the video game Mystery Mayhem (2004). Shaggy and Scooby (once again) refuse to participate in capturing a villain. When Fred asks why they would still be frightened if they knew that whatever monster it would be was just a bad guy in a mask, Shaggy retorts that it's just that: Someone who willingly dresses up in a costume to scare people is not a person you want to be around.
In Zombie Island, there is a whole montage and song about how the ghosts always turn out to be fake. Again, the real villains turn out to not be the case.
Another example in Scooby-Doo! The Mystery Begins: We finally figure out that Scooby Snacks are made with water, flour, eggs, cocoa and dog kibble "for texture". Chocolate is poisonous to dogs. Why is Scooby not dead?
Further lampshaded in the pilot for Mystery Inc., when Velma is giving a tour of her parents' museum, when she drops the bomb on her excited charges that not one of the original series' mysteries was an actual supernatural shenanigan; her parents come along to shut her up real quick after that. All of the gang's parents share the sentiment-the mysteries of the original series have been retconned to have all happened in the gang's hometown of Crystal Cove, and the supposedly supernatural activity ensures a brisk tourist trade; they don't want their kids to keep solving mysteries because they enjoy being employed.
Zigzagged in "Haunted House Hang-Up": To determine which side of a fork in the road the gang should take, Shaggy chooses to flip a slice of bologna:
Shaggy: Heads we take the left side and I eat it, tails we take the right side and I eat it.
Velma: How can you have heads or tails on a slice of bologna?
Shaggy: Heads is the mustard side...tails is plain.
In a scene from "Kooky Space Kook", Shaggy and Scooby lock themselves in a cabin at the airfield, and Scooby tosses the key out the window. The space freak manages to get in by opening the door from the other side. Our heroes run to escape through the locked door but can't get out because Scooby threw the key out. They jump out of the window, grab the key, jump back into the cabin, then unlock the door and escape.
"Mine Your Own Business" has a more perplexing bit. Having found the combination to the hotel safe, Fred offers to read it as Shaggy manipulates the dial. Shaggy proceeds to turn the dial and Fred isn't saying anything except at the end:
Fred: I have the combination...just turn the handle to the left.
Shaggy: Well, why didn't you say so?
A few times, Shaggy and Scooby will see the ghost and sound the alarm, only to be dismissed. How many times have they sounded false alarms to be brushed off like that?