Sawyer did not know Nikki prior to their arrival on the island. He makes the comment 'Who the hell is Nikki' because he has lived on the same island with her for months yet does not even know her name. It is an inside joke as all the audience will also be thinking 'Who the hell is Nikki!'.
Is the Nikki & Paolo story arc an example of fractal storytelling, with Nikki representing the Man In Black and the potential consequences of his plans (mutual destruction)?