What's the reason for discrepancy between DFT calculated image and NC-AFM-acquired one in this article?
1) Most definitely. Adsorbed molecules often are very distorted, up to chemical reaction with support, especially when reactive surface is used. Despite common misconception, even noble metal surfaces are quite reactive.

2) DFT, while being indeed inexact (as any calclation with limited size of basis set), catches major features of electronic density very well.

3) AFM stands for atomic force microscopy, which is not connected to electronic density directly. Now, naphthalene molecule features large $\pi$-system, which is very polarizable. Since nonvalent interatomic forces beyond electrostatic interactions usually increases with polarizability of interacting particles, I would expect $\pi$-systems  to be highlighted on the NC-AFM images.

4) I'm not an expert on atomic-resolved microscopy, but I never read about this possibility in the articles I worked with, though the works I usually works with used STM. and SEM mostly.