Distinguishing Characters

[Mark Knowles]

But if was a superior way to encipher text then surely it would have been very popular. Clearly a cipher as difficult to break as the Voynich cipher would have been preferred to the standard ciphers of that time.

Not necessarily if it was an absolute pain to use. Diplomatic and military cyphers have not always prioritised greater secrecy over speed, to their cost. 

Sure, I agree. This is a point that I discussed in some detail in the presentation that I gave in October.