Halo models provide a simple and computationally inexpensive way to investigate the connection between galaxies and their dark matter haloes. However, these models rely on the assumption that the role of baryons can be easily parametrized in the modelling procedure. We aim to examine the ability of halo occupation distribution (HOD) modelling to reproduce the galaxy clustering found in two different hydrodynamic simulations, Illustris and EAGLE. For each simulation, we measure several galaxy clustering statistics on two different luminosity threshold samples. We then apply a simple five parameter HOD, which was fit to each simulation separately, to the corresponding dark matter only simulations, and measure the same clustering statistics. We find that the halo mass function is shifted to lower masses in the hydrodynamic simulations, resulting in a galaxy number density that is too high when an HOD is applied to the dark matter only simulation. However, the exact way in which baryons alter the mass function is remarkably different in the two simulations. After applying a correction to the halo mass function in each simulation, the HOD is able to accurately reproduce all clustering statistics for the high luminosity sample of galaxies. For the low luminosity sample, we find evidence that in addition to correcting the halo mass function, including spatial, velocity, and assembly bias parameters in the HOD is necessary to accurately reproduce clustering statistics.