It is complex.
I absolutely sure there was Ducky's father, at least in context of original movie.
Why would Don Bluth and Co replace father with sisters?
well, they could, but where's confirmed that adult threehorn next to Topps is his mate? Or Ducky's mother is actually her mother, not her aunt because her mother died?
I'm sure we saw both parents of Cera and Ducky, and lone mothers of Littlefoot and Petrie (and poor Petrie still hadn't his birth scene in introduction, why? We don't even know maybe there was place for his father in early stages of movie)
About Ducky's father absence and skin coloring. Creators of sequels don't dig too deep into details. Character can change its color, its own character can be changed, its siblings can be missing, its actions can be absurd...
but still:
So, on what side do you guys keep the most? hallucinations, or afterlife ghosts?