We study the effects of finite size and of vacancies on the photonic band gap recently predicted for an atomic diamond lattice. Close to a $J_g=0\to J_e=1$ atomic transition, and for atomic lattices containing up to $N\approx 3\times10^4$ atoms, we show how the density of states can be affected by both the shape of the system and the possible presence of a fraction of unoccupied lattice sites. We numerically predict and theoretically explain the presence of shape-induced border states and of vacancy-induced localized states appearing in the gap. We also investigate the penetration depth of the electromagnetic field which we compare to the case of an infinite system.