We don’t have a real answer, there is space to assume he figured things out though.
In the deleted scene, Hook knows that Tamara is with Neal, and that Neal was once with Emma.
Even without that, it is possible he saw them together when pretending to be still knocked out when getting tied up. Or he woke up as they were talking outside the storage locker in Manhattan. Or he overheard Greg and Tamara.
What he did not seem to know for sure was that Bae was Henry’s father.
“If I had a world of my own, everything would be nonsense. Nothing would be what it is, because everything would be what it isn't. And contrary wise, what is, it wouldn't be. And what it wouldn't be, it would. You see?” -- Lewis Carroll, Alice's Adventures in Wonderland & Through the Looking-Glass