To me, "of them" comes across as slightly wrong, because it's partitive. Consider:
- "There were six apples on the table; Susie ate two of them."
- "Susie eats apples often. This morning, she ate two."
A quantity of something implies part of a whole: Susie ate a part of the whole set of six apples. But in the second sentence, which isn't partitive, one would not ordinarily say "she ate two of them".
- "My two sisters go to church every Sunday."
- "Two of my sisters go to church every Sunday."
The of construction in the second sentence clearly suggests that I have more sisters than two, whereas its absence in the first clearly indicates that I have only two sisters.
Similarly with your favorite colors, or the cars of your dreams: you have a fixed quantity, and you're speaking of the entire set. So you might say "Two of my dream cars are a BMW and a Mercedes" if you mean that you also dream about a Porsche and a Jaguar. However, if the first two are the only ones you dream about, you'd simply say "I have two dream cars, a BMW and a Mercedes." Therefore, when answering the hypothetical question, the elliptical form to use would be simply "I have two," not "I have two of them."
As for "there are two": it's better than either of the "of them" alternatives, and there isn't all that much to choose between it and "I have two."