I don’t think Hook would outright tell Emma he was sleeping with Bae’s mother since that doesn’t seem like something you would openly reveal to a potential romantic partner that you had a relationship with her ex’s mother.
I think Emma may figure it out though. She knows Hook loved a woman named Milah and that Rumple killed her. All it would take is for Emma to find out that Bae’s mother’s name was Milah then Emma can put two and two together.
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All magic comes with a price!
Keeper of Felix