But Emma is the Dark One. Just like Rumple or else the many times you’ve tried to stab him through the chest would have worked, Hook. Regina has the dagger in a tree stump (or something); Emma, the Dark One, is safe.
Hook might be referring to how its possible for a Dark One’s host to die after years of using dark magic, and the Darkness could then use their body as a meat suit. That was what almost happened to Rumple, before he had his darkness sucked out of him with the hat.