"A weak encryption can be worse than no encryption" because it gives the communicators a false sense of security (41). As a result, they would fail to conceal their meaning in writing and use plain language.
What's communicated throughout the chapter is that one form of encryption is never enough. If one only employs the method of stenography, the message could be completely compromised upon discovery by the enemy. On the other hand, reliance on one form of cryptography is likewise reckless. Even in Queen Mary's case, as she employs several methods to conceive her message, the secret was still easily discovered.
To keep communication safe through the usage of cryptography might mean multiple forms of cryptography. For example, a substitution mixed with transposition, which adds an additional layer of protection. While that might still be insufficient, one could always choose to hide words by using secret language codes (unlike the codes adopted in encryption). For instance, "to assassin Queen Elizabeth" could be written as "to execute the sailing plan". In Queen Mary's case, such communication could have saved her from facing the death penalty.
Cryptography is only adopted when the messengers can't meet in person, in which case some form of written message has to be created. The key and algorithm, however, are always vulnerable to the risk of being deciphered. Cryptanalysis developed alongside cryptography. Thus, the security of encryption depends on how long it's going to take for the enemy to decipher the code. In other words, cryptography is a highly time-sensitive tool. The complexity of encryption could largely increase security, while also decreasing efficiency to communicate for all parties involved.