That would actually be the most logical explanation out there. I'm not sure if Littlefoot knows how the circle of life works, that you need both a male and a female to create a child. If he had known that, I'm pretty sure he would have asked about the whereabouts of his father. If he didn't know that, and he saw all his friends with mostly single parents, he may not have thought of a father at all.
If he never asked, I assume they just let it rest for his own well-being. What would Littlefoot have done if he lost his family, but knew that there may have been a father out there looking for him? He may have started looking for his father instead of the Great Valley, out of pure curiosity. His father would after all be more exciting to see than his grandparents.
If he never knew that fathers were required to get a child, and they never told him either, then I guess he would have been very surprised!

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PS: I know technology these days makes it possible that you don't need two to get a child, but we're talking prehistory here
