We generally don't bother to encrypt messages if we have nothing to hide. By using a code or cipher, it's implied that the contents are sensitive or illicit in nature. In fact, as Singh points out, they're likely to be more explicit because the encryption lulls the sender into a false sense of security and they write more openly about their plans. So by putting too much faith in an easily breakable cipher, you risk incriminating yourself further.
In addition, by using a cipher or code that is easily identifiable as such, you automatically invite suspicion. In her trial, Mary claimed she knew nothing about the plot, but even without decrypting the message, it was clear she was corresponding with conspirators. Also, the fact that she didn't write her message in plain text implies she was concealing something. In situations like these, it may be better to stick to some sort of code that masks the message as something innocuous, or some sort of steganography that hides the secret message within another. By finding a way to hide a message in plain sight, it helps divert suspicion in the first place rather than relying on an imperfect cipher once you've drawn attention.