I'm more of a mind to say that SW just can't keep track of everything it ever had created for the show. There's thousands of hours of footage, thousands of episodes... I don't think they have the money, resources, and manpower to sift through all that, especially when everything has multiple sketch names inconsistent with their actual archival titles.
What some kids find scary is eye of the beholder stuff. Kids have weird fears that can go all over the map, and a sketch one kid can find horrifying another can find perfectly alright. Cracks does seem like something that can creep a kid out, but I don't think they'd get enough complaints or bad reactions from the short to have it pulled. I mean, if it tested poorly before hand, it simply wouldn't have made it into the show. I doubt they willfully pulled it, and it's more of a case of just being lost in the shuffle and being passed over for more popular, kid friendlier sketches. Not all lost Sesame Street comes off as a creepypasta. Lots of lost Sesame is very banal and inoffensive. Like Leslie Mostly. Those are just dull and forgettable.
That said, that's a very interesting story behind how Cracks was found, some of us actually remember it going down right down to the note from the animator mis-attributed to it. I even said "Hey, you may not have the Cracks video, but you got an original sketch of Scooby-Doo from one of his animators." Can't lie, I'm more jealous of that than getting that random clip.
But the story I want to hear is how the heck Seven Monsters, a sketch that was reportedly never on the show, fell into our laps with no inquiries or even so much as a request.