Is this phrase exclusively meant with reference to sons similarities with their fathers or can it also be used to refer to "daughters and mothers" or "daughters and fathers" and other relations like uncles, nephews ?
The phrase doesn't necessarily have to refer to a father any more. As the Phrase Doctor mentions, it means:
The site does mention that the phrase is usually meant to refer to a father, but that it isn't the only meaning:
So, you can feel free to use it to refer to the similarity between a child and either of their parents. However, I wouldn't necessarily use it to refer to a child and another family member: it is more understood as referring so someone's parentage.
Its actual meaning is "a child who is similar to one or more of its parents."
So yes, it could be used for daughters too.