After the execution of Mary Queen of Scots but prior to the development of more complex ciphers, like the Vigenère cipher, "anybody sending an encrypted message had to accept that an expert enemy codebreaker might intercept and decipher their most precious secrets." (Singh, p. 45) Because of this, it is safe to assume people writing the encrypted messages would still be very careful with what they were actually saying, and how the things that they wrote could potentially incriminate them. Messages would have been written in vague enough language that even if the text were to be deciphered, the cryptanalysts would either not be able to tell what the exact plan was or, even if they could figure it out, would not be obvious enough to be used in a court of law. (I don't know how the rules for this worked in that time but today people can claim the way a message is interpreted is completely wrong.)
Going off in a completely different direction now, as I was reading I was thinking of different types of ciphers. When I the name Louis XIV, I fixated on the Roman Numerals. It made me curious about the use of Roman Numerals in cipher alphabets. I think it would add a layer of complexity because the cryptanalysts would have to try to figure out which combinations of letters would represent a number, and then which letter was represented by that number. One weakness, however, would be that it would be very easily identifiable as Roman Numerals because of the small number of letters used in Roman Numerals. I tried to look up Roman Numeral ciphers but nothing came up on a quick Google search.