I always felt that Junior knew since she was a child who Jack really was to her father. After all, she could easily see the transformation her father underwent a few times each year, right before he left on one of his trips, and right after he'd returned. By the time she was an adolescent, I'm sure she'd figured out that the reason this guy Jack made Ennis so happy is because he was her father's true love, she could easily see he was the only person who could make her father feel that way. And I believe she felt happy for her father the he had true love, but also sad because she could also see how miserable and alone he felt when he was apart from Jack. I always thought that Ennis and Junior are a lot alike, they might not always say what they are thinking or feeling, and therefore it may be difficult for the people around them to figure it out, but they are feeling inside, and Junior in her quiet way lets her father know that she understands.