A question that might be asked is why would a hidden author use such a simple cipher if he didn’t want to his authorship to be easily detected? The answer is that a simple cipher makes it relatively easy for one to figure out what kind of cipher may have been used. And it could still be difficult to detect by using it in creative ways that blend in with a normal looking text. This was actually practiced in Elizabethan espionage. On page 287 of The Watchers by Stephen Alford, 2012, we find, regarding a letter by an agent of Thomas Phelippes “But woven into the letters were passages of cipher.” Then on page 290 of this book is a quote by Bacon writing to Phelippes of how he [Bacon] could learn from him, “And indeed I would be the wiser by you in many things, for that I call to confer with a man of your fullness”.
The other alphabet that early Baconians found is what they call the ‘Kay’ cipher. This is a more complex cipher and may have been used for some purpose beyond that of the simple cipher. The early researchers looked for it based on Bacon’s mention of a “Kay-Cyphar” which he didn’t describe. The Baconian cipher hunters had reason to believe that this cipher was based on the letter ‘K’ in the alphabet, as the first letter in this cipher. The Friedmans faulted this analysis, saying that the ‘Kay’ that Bacon mentioned didn’t refer to the letter ‘K’ but was just an alternate spelling of the word ‘Key’. They said this is clear because Bacon used an ‘a’ for an ‘e’ five times in the same passage. In the page long passage that Bacon wrote, he spelled ‘Cipher’ (with an ‘e’) and ‘Ciphar’ (with an ‘a’) each about a half-dozen times. But the ‘pher’/’phar’ syllable doesn’t seem comparable to the ‘kay’/’key’ syllable.
In the 1640 edition of the Advancement of Learning (interpreted by Wats) we find on page 264 the phrase “Kay-Cyphars”, as well as the spelling “Cyphers”. In the 1623 Latin edition of the book Bacon did use “Ciphrae Claves” where ‘clavis’ is Latin for ‘key’. And even the early Baconian (Mr. W. E. Clifton) who ‘discovered’ what is now called the Kay cipher, and who had seen the 1623 edition, himself thought for a time that this may be the case and said that “…the words “Ciphrae Clavis” probably meant “Key” Cipher rather than “K” Cipher.
Personally, the “Kay”=”K” (and not “Key”) interpretation looks more right to me, or maybe he meant the “Kay” alphabet as one type of “Key” cipher. Bacon knew the difference between “Kay” and “Key”. He used the word “Key” in a letter to King James saying “And again, for that my Book of Advancement of Learning may be some preparative, or Key, for the better opening of the Instauration,….” And since Bacon didn’t go on to describe the “Kay-Cyphar” that he mentioned, he may have wanted to keep it secret. Also, there are rational reasons for a cipher or code alphabet to begin with the letter ‘K’. It’s the first letter in the straight alphabet with two digits and so has the advantage of using all letters represented by two digits and avoids the confusion of whether something like the number 21 represents the letter W or the letters BA.
One other of the Friedman’s criticisms of the Kay Cipher was that Woodward (one of its users or discoverers) does not explain why the letter ‘A’ does not have the value 25, following ‘Z’ as 24, as one might expect. The only explanation that he said has so far been offered is that the value 25 is assigned to ‘&’, and 26 to another letter ‘E’.” The Friedmans called this an “eccentricity”.