this feature is also available in the free edition! Before creating a new encrypted folder with BoxCryptor activate Advanced Mode in the preferences and click ok. When you are prompted to type in a new password, you can now see advanced settings including filename encryption. Just uncheck this option. Now your filenames will not be encrypted in this directory.
PS: If you need to change the filename encryption on an already encrypted folder, you can use our small command line utility BoxCryptor Control. See http://blog.boxcryptor.com/boxcryptor-beta-091-released