Quote 1
"Let me see your eyes! […] No, your real eyes! Those fakes don't fool me any more than your ridiculous lie about Abe!" (5.122)
Emma wants to see Jacob's eyes because wights—some of the bad guys—don't have pupils. It seems that Emma knows that wights can alter their eyes, too, which makes it a little less surprising to learn that Dr. Golan hid his identity with contact lenses to make his eyes appear human.
Quote 2
"Nobody suspected a thing," [Emma] said. "People come to sideshows to see stunts and tricks and what-all, and as far as anybody knew that's exactly what we showed them." (7.37)
When most people see something that appears impossible, like a levitating person, they assume it's some sort of magic trick, not an actual supernatural power.
Quote 3
"I know he would've been proud of you," [Emma] said. (10.338)
This is nice of Emma to say. She knows that Jacob would have done anything for his grandfather's admiration while Grandpa was still alive, so she gives him a little taste of it.