I could see CaptainSwan occurring because even with Hook loving Milah whose son was Bae whose son is Henry whose mother is Emma; they are not actually related. Not by marriage, not by blood, not by any standards what so ever, it would be weird and I’m sure Snow and Charming would kill Hook before letting it happen, but I could see it coming.
Bae never saw Hook as his father so CaptainSwan is not as “weird” as SwanQueen would be. If Rumple and Emma hooked up, that would be weird because Rumple is Bae’s father so Rumple is kind of like Emma’s father in law but not officially because Emma didn’t marry Bae but the connotations are still there.