Quote: "is there any way to encrypt files in AppGameKit?"
Yes, but nothing built in.
Quote: "you can encode the files with a self made tool"
Quote: "You will have to write your own encryption routine"
Quote: "Steve Vink posted an article on encryption/decryption with example code"
If you convert an image to a memblock, you can apply any encryption you like, but you will have to write the code to do the encryption and decode.
Pseudo:
Loadimage
create memblock from that image
encrypt the new memblock (with your own function)
save the encrypted memblock
In your game:
Load encrypted memblock
decrypt memblock (with your own function)
create image from memblock
Hopefully we will see media folder encryption built into a future release, where can can just set a key at compile time. That would be SO nice!