We don't know as of now what has happened in Storybrooke in the passing years, but I think unless told differently, you can assume that Emma and the real Hook are happy there. I do wonder how they'll explain why Emma and real Hook aren't searching for Henry and Regina because they should lose touch with them once the curse hits, but that is a discussion for later in the season. But for now, I think you can assume they are safely in Storybrooke especially since it seems like Jen is not open to coming back to do follow-up episodes.

I think it was very anti-climactic for a character who was such a big part of the show. I think that ending was more about preserving Captain Swan than it was about Emma. They wanted a way to free up Hook for future storytelling without breaking up he and Emma. And I think a wish Hook and Regina pairing would be very awkward. He is too strongly associated with Emma, even in an alternate version, and Emma and Regina are friends. I'm fine with them each getting new love interests, but I don't think it should be each other. I also think it might happen anyway.