The status quo of cryptography can be accurately represented by a game of tennis between two equally good players. When a strong cipher is developed, the ball moves to cryptanalysis. Upon development of better decryption techniques, the ball returns back to the court of the encryptors. The period in which an event happens in the world of cryptography is heavily influenced by who has the power between cryptanalysis and encryption.

During the time of Mary Queen of Scots, the users of cryptography had little to no faith in the abilities to decrypt, causing them to have  undue faith on their abilities to encrypt. By not giving sufficient credit to cryptanalysis, they did not bother with either reinforcing the difficulty of the cipher  or any sort of counter measures in case the cipher was broken, leaving them in a worse position had they chosen not to encrypt. On the other hand, the situation before the Vigenère cipher was the exact opposite as the strength of any cipher was presumed to be weak. Encryptors were motivated to fortify their ciphers and even after encryption, they would communicate in  ways that would seem senseless without context. Some would even avoid cryptography altogether and find other ways to convey the desired message.

I also believe that during the period of Mary Queen of Scots, cryptography itself was fairly new and unheard of. This meant that almost no one had any idea how to encrypt (and naturally, decrypt) ciphers. After cryptography became more popular, more people explored the avenue and cipher breaking became more ubiquitous. This was another reason for encryptors to strive to strengthen their ciphers.