Part 1
Since Bob does not know a specific output given a specific input, he must use the inverse of the secret matrix.
Part 2
I believe that Eve should be able to decrypt the message by using the fact that the system is linear and time invariant. The linearity of the system can be seen in the use of decoding with the matrices:
The system is obviously time invariant because it doesn't matter what time you evaluate the encrypted code with the secret matrix, it will always give you the same output. I'm not exactly sure how she would do it, I need some time to think about it. Does anyone have any ideas? Or is this completly wrong?