Even if they do mean that Hook’s “set his sights on her” in a romantic context, that doesn’t automatically mean that Emma’s gonna see him in the same way. They didn’t say, “they have set their sights on each other.” With Ariel’s story being told in the first part of the season, there’s gonna be unrequited love in the air in flashbacks, (even if Onceiverse Ariel and Eric do get together, their story still traditionally starts out as unrequited love), and they could maybe plan to expand on that theme in present day if Hook has eyes for Emma but not vice versa.