This modifcation might be a bit dangerous to your Due. Basically what you do is connect SPI signals to other IO pins of the same micro directly. It is probably ok as long as the IO pins remain in high impedance state, but if you accidentally set them to high or low levels you may encounter problems. It is something you should not do in hardware.
I would recommend that if you really want to use the Adafruit Datalogger shield on a Due, then you should at least cut pin 11, 12 & 13 of the shield. Or at least run the MOSI, MISO and SCL through a 1K resister.