It would say that it was a bad relationship for Emma. It has been written as a bad relationship. They are not true loves and Emma has lost part of herself by being with Hook. If this show made sense they would break up. This show does not make sense so that will not happen. I am not saying that what is logical will happen, but what would be well written and logical exists outside of what is actually happening on the show.
I have seen many shows where characters date for years and then break up because relationships don’t work out, people change, people want different things out of life. It is not a stretch. Their relationship is toxic and should not exist. If this show was about characters that were written like real people, then that is what would happen.
Also, Emma and Hook have only been dating two seasons, not three, or two and a half now, sort of and it has been what six months in timeline, so it isn’t the end all, be all of relationships. Also, this is the safe place where we can say that Emma being with Hook is bad and we want her to be with Neal because guess what they make way more sense then Emma being with Hook.