What do wicked things mean in fiction?
If Daniel Handler depicted Count Olaf as the fictional counterpart of Moses, then "A Series of Unfortunate Events" would have been an exaggerated, if not misleading, news feature from The Daily Punctilio. Geraldine Julienne, the reporter of that newspaper, could have been a responsible journalist. And the inhabitants of the Village of Fowl Devotees might not have been a bunch of blind followers. All thirteen books were a series of smokes and mirrors, where a troika of siblings grew up faster than they should.
Why would readers want to read about injustice? What could they learn from the misfortunes of three children? Doesn't Handler believe in fairy tales?
Handler wasn't the first to pen a dark story with wicked characters, as this literary device would go way back to the tragic lives of Greek demigods. These authors weren't sending a strong message that it was a bad world out there and the good ones would be advised not to go out of their comfortable houses. They wanted to see how their readers react. They wanted to show how their characters deal with such circumstances.
In the case of the Baudelaire children, readers would cheer for their resilience. They would be amazed at their good fortune of meeting good characters, even if the series suggested that the bad guys outnumbered them. Handler loved literature, as several minor characters were popular enough. (If you happen to be a student of literature or a heavy reader, then it won't be a problem.) This would lead to the final question.
"A Series of Unfortunate Events" may look like a fairy tale in the surface, but it was more of a riddle that could entertain (or irritate) readers. "The Penultimate Peril", the twelve book in the series, began with Violet, Klaus, and Sunny meeting Kit Snicket for the first time. She was the sister of Jacques Snicket, who was framed for murder in the Village of Fowl Devotees. (She was also the sister of the narrator, who was searching for the Baudelaire orphans.) Kit's explanation would be reminiscent of the Bible; the world was once populated with good people. Trivial matters led to a schism, where some heroes became traitors. And then there were volunteers who gathered evidence of their good deeds (and criminal offenses).
Kit, who happened to be giving birth anytime soon, left the trio in Hotel Denouement. She promised them that their misery would end soon, as their guardians and the bad guys should meet in the hotel on a Thursday evening. There would be a court trial, where Olaf and his cohorts were expected to get their prison sentence (or so they thought). At this point, readers knew too well that wickedness prevailed one more time. Violet, Klaus, and Sunny became more confused than ever.
Handler didn't let his readers go on a wild goose chase, as there were reasons behind this strange scenario. What was significant about Hotel Denouement? Richard Wright couldn't stay there and penned his masterpiece. It happened that the father of the (Baudelaire) kids often recited lines from Wright's books. It might be the clocks, which blared WRONG! WRONG! WRONG! every 3 PM. The Baudelaire kids have the chance to meet an orphan, albeit briefly. He was a good soul, but an accident caused his demise. The children might have found their happy ending if they accepted the offer of a masked man (to drive them away from the hotel). There were chaos and mystery, which would mark the penultimate chapter of previous books. A pattern could be found there, another ending would bring the readers to the next book. The twelve one seemed to be definite, and it had nothing to do with the title.
Handler was thinking of a figure of speech, and it would be up to readers to figure it out. Pleasant surprises await them. Justin Timberlake might be the only one missing in the picture, as he was supposed to serenade the kids with "Cry Me a River".

