Light propagation in disordered media is a fundamental and important problem in optics and photonics. In particular, engineering light-matter interaction in disordered cold atomic ensembles is one of the central topics in modern quantum and atomic optics. The collective response of dense atomic gases under light excitation, which crucially depends on the spatial distribution of atoms and the geometry of the ensemble, has important impacts on quantum technologies like quantum sensors, atomic clocks and quantum information storage. Here we analyze near-resonant light transmission in two-dimensional dense ultracold atomic ensembles with short-range positional correlations. Based on the coupled-dipole simulations under different atom number densities and correlation lengths, we show that the collective effects are strongly influenced by those positional correlations, manifested as significant shifts and broadening or narrowing of transmission resonance lines. The results show that mean-field theories like Lorentz-Lorenz relation are not capable of describing such collective effects. We further investigate the statistical distribution of eigenstates, which are significantly affected by the interplay between dipole-dipole interactions and position correlations. This work can provide profound implications on collective and cooperative effects in cold atomic ensembles as well as the study of mesoscopic physics concerning light transport in strongly scattering disordered media.