The root "books" folder is for you to sideload books that you download from Amazon's website. (Not very useful for an internet connected tablet.)
Books that the device downloads itself are in deeper in the folder tree. On my Fire tablet there is a folder for each book named:
\Fire\Storage device\Android\data\com.amazon.kindle\files\Books\ amzn1.account.{account#}\{ASIN}
Most books these days will be in KFX format using a file-naming conversion that is not supported by calibre. Also, there is no way to remove DRM from books on a Fire tablet even if they are recognized.
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