This is an interesting debate; Do you have the kiai of uke muted, because the Tori is the winner of the previous match and he deserves to show that off by shouting at his opponent to do better than the previous one, or do you mute the Tori's one because uke is the new challenger and he issues, as groh said, a challenge to the Winner...
Then again you could have each kiai played one after the other, with uke starting, issuing a challenge and Tori responding.
A Kiai is usually a shout issued when performing an attacking move, as it channels your Ki . In my opinion uke's kiai should play, because he is the challenger, and at some point the Tori was probably a challenger too, so we've heard his kiai already.