Emma is only a sex symbol. Jean was girl next door. Scott/Emma's relationship is based purely on sex.
Everything in X happens all at once, he didn't have time to investigate what Scott was up to when he refused to tell Henry what he was doing with the time devices. If he knew, Henry wouldn't put up with the death squad. But jeez, Scott didn't tell Emma either, and she has almost no respect for boundaries, but more important, she wouldn't have stopped him! She'd have helped him! On the other hand, Emma is oddly bad at keeping secrets--you can tell when she's holding back. Scott keeps everything secret. It's all about the security!