It's Not Easy Being Green - S3-E16
Continuity mistake: When Hook is at the beach with Henry, after he says to him, "Fair enough, mate", the pendant on Hook's necklace goes from resting against his chest, to being partially tucked under his waistcoat. In the close-ups, the pendant is completely covered by the waistcoat. (00:26:50)
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.