Current capsule implosions at the National Ignition Facility (NIF) using high-density-carbon ablators and laser energies close to 2 MJ have shown neutron yields in excess of 50 kJ. Improving on this performance requires understanding of the different degradation mechanisms. For many NIF implosions, nuclear diagnostic signatures have inferred residual hot-spot velocities that correlate with fuel areal density variations consistent with a low-order mode-1 asymmetry. A current working hypothesis attributes these asymmetries to a combination of beam to beam variations in the laser delivery and possibly coupling to target features, such as the diagnostic holes needed for x-ray imaging. Recently, a new source has been identified, thickness variation in the ablator shell. To gain better understanding and eventually mitigate the causes of asymmetries, 3D integrated simulations using the actual delivered laser powers are needed. To capture the effect of the diagnostic holes (DHs) using direct numerical simulation would require significantly large computational resources. Instead, our 3D simulations make use of a subgrid model developed using highly-resolved 2D simulations that include several details of the DH engineering complexity. Simulations of NIF shots using hohlraums without DHs, to isolate the effect of beam-to-beam variations, reproduce fairly well the observed nuclear diagnostic signatures. Similarly, reasonable agreement between data and simulations is also obtained in the presence of diagnostic holes. To account for the remaining discrepancies a sensitivity study of ablator thickness variation showed that 1% thickness asymmetries are comparable in effect to 1% peak drive mode-1 asymmetries. Additionally, this study identified sensitivity to variations in the imbedded doped layer (needed to shield the DT ice from the high energy x-rays generated in the hohlraum) thickness even when the inner and outer surface of the ablator are perfectly spherical.