Another reason could be for marketing purposes. A unique and somewhat mysterious title like 'Cloud Atlas' stands out. It doesn't really tell you that the book contains six interwoven stories across different time periods and places. But it catches people's attention and makes them more likely to pick it up and start reading to find out what it's all about.
There's 'Catch - 22'. The title doesn't give any hint about the absurd and nightmarish military bureaucracy and the various characters' plights during World War II that the story is actually about. And 'Brave New World' is also such a title. It doesn't directly tell you about the dystopian society where people are genetically engineered and conditioned to fit into a pre - determined social hierarchy.
It depends. Sometimes short story titles have quotes, especially if they're a direct quote from someone or something within the story. Underlines are less common.
It varies. In some cases, short story titles may have quotations marks, especially if they are presented within a particular context or style. But there are no strict rules that apply universally. It could also depend on the genre or the preferences of the author or publisher.