Your question is interesting because, in fact, both "theme" and "topic" can often be used as synonyms of each other.  In regards to "Paper Towns," the main theme is one of superficiality (both in love and in hometowns).

Why is the theme one of superficiality in love?  Because the main character, Quentin, spends his entire young life being in love with his first sweetheart, Margo, but finds out during the course of the story that she is not the person he thought she was.  There are clues throughout that this is the case.  Quentin is intelligent and less likely to take risks while Margo is "cool" and more likely to take risks.  Take, for example, the night when Margo shows up at Quentin's window before high school graduation.  Margo has a night of revelry planned.  Quentin hopes it will cement their relationship, but Margo leaves, requests to be found, and Quentin finds himself while pursuing her.  Ultimately, he finds out that Margo is not for him.

Why is the theme one of superficiality in hometowns?  Well, this story is about the challenges in the culture of central and south Florida.  There is too much development, too much heat, too many temptations, too many cookie-cutter neighborhoods designed to eventually fail. These are the "paper towns" that are meant to fall apart.  Quite true in my own experience in growing up in South Florida.

Thus, you can see the main theme or main topic of the story is certainly superficiality in relationships and towns.  Quentin finds out the truth of this main theme during the course of the book.