Firstly, let's assume that directories aren't encrypted. Otherwise this would be a real PITA - just to locate /foo/bar/baz.txt you'd have to decrypt each component of 001001/011101/110101.encrypted separately.
More importantly, the decrypting software has no way to encrypt things, only decrypt them. So to read 'secret.txt' you can't just encrypt 'secret.txt' to '111000.encrypted'. Instead, you have to iterate through the entire directory listing and decrypt every single filename, until you find one that decrypts to 'secret.txt'.
Obviously this gets pretty bad with even moderately-sized directories. I assume this is why the project doesn't encrypt filenames.