We study the effect of long-range disorder created by charge impurities on the carrier density distribution of graphene-based heterostructures. We consider heterostructures formed by two graphenic sheets (either single layer graphene, SLG, or bilayer graphene, BLG) separated by a dielectric film. We present results for symmetric heterostructures, SLG-SLG and BLG-BLG, and hybrid ones, BLG-SLG. As for isolated layers, we find that the presence of charged impurities induces strong carrier density inhomogeneities, especially at low dopings where the density landscape breaks up in electron-hole puddles. We provide quantitative results for the strength of the carrier density inhomogeneities and for the screened disorder potential for a large range of experimentally relevant conditions. For heterostructures in which BLG is present we also present results for the band-gap induced by the perpendicular electric field generated self-consistently by the disorder potential and by the distribution of charges in the heterostructure. For SLG-SLG heterostructures we discuss the relevance of our results for the understanding of the recently observed metal-insulator transition in each of the graphene layers forming the heterostructure. Moreover, we calculate the correlation between the density profiles in the two graphenic layers and show that for standard experimental conditions the two profiles are well correlated.