I tink it's safe to assume Corvo definitely is her father.
As stated previously, the Empress and him seemed very close right from the beginning, Emily noting her mother seemed sad when he wasn't around. Overheard rumors and some written notes also contributes to this thesis - did you find the very small room hidden behind a fireplace in the Tower? There was a rune to grab there, as well as an audiograph from the Empress to her daugther, and a letter adressed to Corvo by the Empress, barely withholding her feelings toward Corvo.
No mention is ever made of the father or a possible Emperor, even a late one.
Havelock's final journal entry clearly asks the question "Is [Corvo] really her father?" which, while not directly answering the question, is quite a dead giveaway when you consider every little clues there was on the path.
The final words of the Outsider in the good ending, " you were always more than just her protector " ( paraphrasing ) is an ultimate, small, cruel teasing
