Tougher Than the Rest - S6-E12
Visible crew/equipment: When Sir Henry searches for his mother and The Evil Queen along the water's edge, in the shot where he says, "They crossed the river", as he turns his horse around, a horse wrangler's hand can be seen holding the horse's bridle in the lower half of the screen, guiding the horse to turn around. (00:04:20)
Answer: He knows who she is because he knows that the fairy tales are true. He was also shown to sneak out to go see Emma or someone else. Sometimes he succeeded, sometimes he didn't. This is how he knew to look for her despite his strict mother.