Wilke of course brought up the same thing as we all know. You could tell even then she knew but was denying it. I actually think she was subconsciously (some may argue it was consciously) taking advantage of the fact that Emmett liked her. She knew he would always come running when she asked.
I personally don't think it makes sense at this point for Daphne and Emmett to ever be together after what happened with he and Bay. He realized he would be settling with Daphne so to go back to that wouldn't make sense for him. However, the writers might decide to temporarily take this route anyway. I just hope they keep them frienRAB and frienRAB only. I hate it when they make the endgame couples (and this is what I think BE are) recognize the truth about each other and the significance of their relationship and that they are are with the right person, only to have them go back on that later and act like this never happened. Then they have them instead go back to the "safe" option which they know is safe.
A prime example would be Dawson's Creek. Daphne=Dawson, Emmett=Joey, Bay=Pacey. I am actually watching Dawson's Creek again for old time sake and I am at the episode where they all visit Dawson's Aunt Gwen and she tells Joey about how the guy she was married to for years was "safe" and she basically settled for him because it was "comfortable." Then she met this guy Richard who brought her to life and he was the love of her life so she left her husband for him. Of course this was meant to represent Dawson, Joey, and Pacey. Pacey made Joey feel alive and more than she ever thought possible, while all she would be doing is settling if she picked Dawson because that was a safe love. I see the same thing on this show and I am sure it is because the same producer made both shows. Bay makes Emmett feel alive, free, and so much more than he ever felt for Daphne. But that is also the scary kind of love isn't it? That is the kind where you truly make yourself vulnerable and put yourself out there. It is the kind where you take that huge risk and step into a world that frightens you. Joey on DC, ran away from it as she said in the finale because of how powerful it was. Emmett could have ran away and picked the easy and safe choice in Daphne but he chose to take that risk and he will be far more fulfilled in life because of it. There is no going back after that imo.