It seems to me that, if the facility to encrypt file and folder names us available to you, your default should be to make use of it. Recall that the purpose of enlisting Boxcryptor is to prevent non-authorised people from gleaning any understanding of your data.
The basic idea is to protect your files from prying eyes. Unencrypted names can tell a snoop alot even if the files, themselves, are encrypted.
To pick a clear example let's say you have the following folder structure:
If someone came snooping, you can see that problems may follow. Encrypting filenames (and file types) is just as important.