An hour? You've made my case. It takes at most a couple of minutes for importing hundreds of books in Calibre. Metadata retrieval is automatic (from the file itself and/or online). Everything happens in a few clicks.
With a file manager, you'll probably only be able to find a book from its author, and title. If you have a small collection, this is fine.
When your collection grows though, issues start to show up. Being able to sort, and find a book based on other information becomes much more useful: date of publication, genre, custom tags, etc... While you could always integrate these in your filename/directory structure, with the help of symlinks, it's very cumbersome to manage and use.
An hour? You've made my case. It takes at most a couple of minutes for importing hundreds of books in Calibre. Metadata retrieval is automatic (from the file itself and/or online). Everything happens in a few clicks.