Throughout Gatsby’s courtship, or wooing, of Daisy he holds fast to the belief that he can change the past. He believes he can simply wipe out the past several years by winning over Daisy and then living happily ever after. When he sees Daisy’s child, he is looking at physical evidence that the past does exist and it cannot be changed. She is proof of Tom and Daisy’s relationship and she is proof of previous years. He is shocked because this thought never occurred to him, that the past relationship between Tom and Daisy is something concrete that will always exist.
A child is often a product of love, which he hopes is not really going on with Daisy and Tom. A child means at least 18 years of permanence between a man and a woman even if they separate.
Daisy also lives a life apart from her child. He's seen Daisy in many situations, but not ever with a child. This child suggests Daisy is not just a wife to be separated, but a mother. I think if there was any moral bone in Gatsby's body a child would give cause to think twice about what he intends to do.
I think he also would have liked to contribute to the children that Daisy would have.
Nick says that Gatsby likely never believed in the child's existence. The reasons above, to me, are likely why.
The answer to this question can be found in Chapter 7.
What Nick Carraway, the narrator, says is that Gatsby has never really believed that the girl (Pammy) was real. Up until this point he has sort of tried not to think about the child.
I think that what is going on here is that Gatsby is starting to have to face up to the fact that Daisy really does have this life that she has made without him. He has been assuming that she could just come and become his, but now he sees her child and I think he starts to realize it's not going to be that easy.