I agree completely that the tag question version suggests the speaker believes the person has two sisters.
If you don't already think this, it's very unlikely you'd guess that a question out of the blue.
Person A: I wish I had a sister who helped me with my homework the way yours does.
Person B: You have two sisters, don't you?
Person A: Three actually... but none of them are any good at math!
How can you imagine "Do you have two sisters?" being used aside from "Hey, guess how many kids are in my family!"?