Distinguishing Characters

[tavie]

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. 

Also we do not know just how impenetrable the manuscript would have appeared to a hypothetical, motivated "unauthorised reader" who stumbled on it around the time of its creation who might have a reasonable idea of the language inside it and its content.  If knowledge of these points weakened its strength, that would also harm its value in the balance against ease of usage.

So I would hesitate to call the system "superior".