I don't think she read his mind so much as spotted other signs he was sick: flushed cheeks, sweating, he was acting kind of unnaturally. If he was actually sicker than he thought, sometimes sick people have a certain smell. She probably also noticed from his body language that Nishikata was clearly trying to hide something and eliminated/couldn't think of other possibilities. From thereon, she guessed he was sick, and happened to be right.