Illana might have been his daughter in the script at one point, but the show is what matters, and in the show, she is not. She says Jacob was "the closest thing I ever had to a father". I imagine they just cut the story line, but in the same way Smokey's name might have once been Samuel on paper, it's not mentioned in the show, and until a canon piece of media is released with that in, his name is not Samuel.
I do wonder what was cut this season. At ComicCon it was shown that sideways Kate didn't kill her father, she was accused of killing his apprentice instead, in this season she claims to not be guilty, and never mentions who she was meant to have killed. The Illana thing was cut too it seems. I don't really know how they wouldn't know from the start which stories they could, and couldn't include this season.