I think Pearl would have sensed the change in her mother, though subtle, every time she was around dimmesdale. Though hawtjorne doesn't go into detail in this ONE area, you know since he was her minister they would have had contact with one another at least weekly, all of Pearls life. Kids can really pick up on the body language of their family members and I think that is what the author portrayed when commenting on Pearls seemingly innate ability to see the connection between arther and hester.