Resposta curta: foi uma decisão da editora americana. A edição européia sempre teve o capítulo final.
Da Wikipedia:
The book has three parts, each with seven chapters. Burgess has stated that the total of 21 chapters was an intentional nod to the age of 21 being recognised as a milestone in human maturation. The 21st chapter was omitted from the editions published in the United States prior to 1986. In the introduction to the updated American text (these newer editions include the missing 21st chapter), Burgess explains that when he first brought the book to an American publisher, he was told that U.S. audiences would never go for the final chapter, in which Alex sees the error of his ways, decides he has lost all energy for and thrill from violence and resolves to turn his life around (a slow-ripening but classic moment of metanoia—the moment at which one's protagonist realises that everything he thought he knew was wrong).
At the American publisher's insistence, Burgess allowed their editors to cut the redeeming final chapter from the U.S. version, so that the tale would end on a darker note, with Alex succumbing to his violent, reckless nature—an ending which the publisher insisted would be 'more realistic' and appealing to a U.S. audience. The film adaptation, directed by Stanley Kubrick, is based on the American edition of the book (which Burgess considered to be "badly flawed"). Kubrick called Chapter 21 "an extra chapter" and claimed that he had not read the original version until he had virtually finished the screenplay, and that he had never given serious consideration to using it. In Kubrick's opinion, the final chapter was unconvincing and inconsistent with the book.
Fonte: Wikipedia