We theoretically investigate the effects of long-range disorder and electron-electron interactions on the optical properties of hexagonal armchair graphene quantum dots consisting of up to 10806 atoms. The numerical calculations are performed using a combination of tight-binding, mean-field Hubbard and configuration interaction methods. Imperfections in the graphene quantum dots are modelled as a long-range random potential landscape, giving rise to electron-hole puddles. We show that, when the electron-hole puddles are present, tight-binding method gives a poor description of the low-energy absorption spectra compared to meanfield and configuration interaction calculation results. As the size of the graphene quantum dot is increased, the universal optical conductivity limit can be observed in the absorption spectrum. When disorder is present, calculated absorption spectrum approaches the experimental results for isolated monolayer of graphene sheet.