There are many ninjas in this picture, but only one is visible.
There was a rather elaborate pagoda where an empty lot used to be. Yuffie stood on the front steps of said pagoda, and looked around herself with utter confusion, and wished that she wasn't stuck wearing the formal robes and makeup required by her position, because she had no clue what the hell was going on right now.
Despite the fact that she wouldn't be able to move or fight particularly well just now, or the fact that almost everyone in said pagoda had apparently vanished, she wasn't too nervous.
She could tell that she still had her ninja bodyguards, after all. Not that they were, you know, visible.