First thing, chemistry is reaction between molekules, which you will never be able to see. So you can't see chemistry between the two people LITERALLY
And yeah, there certainly is chemistry between Shinichi and Haibara, since She developed APTX and Shinichin shrunk because of that. Yep, chemistry indeed. :3
And now for a serious answer (sorry ): I don't think Haibara and Conan fit together at all, because the way they think is too different.