Originally yeah, in first early builds of the game it was implied that Nami was basically the MC’s biological sister. I’m pretty sure Nojiko was even referred by them as a mother in those first releases. I don’t remember if she was ever meant to be blood-related or if it was more of a “she raised them so they call her mom” kind of thing.
As the story developed, Ocean ended up rewriting that part. In the current canon, none of them are blood-related. Nami and the MC are just roommates, and Nojiko is adoptive mother figure. The MC’s parents died in a car crash, and Nojiko stepped in and took care of them, since I believe she was a close friend of his mom.
As for patches: There's
Uncut Mod, where the taboo version restore MC and Nami as siblings.