With "nicht" immediately before the verb, I believe there is a subtle but important change if the meaning.
The speaker then would be saying that the person will not say "yes"... but would perhaps, for instance, write it.
I hope a native speaker could confirm or deny my interpretation. Thanks...
German does: http://german.about.com/library/weekly/aa031901a.htm
But this sentence could be about the concept of assent rather than the word "yes", so "ja" is used without quotes as it is not a quoted word.