A unique differentiation in your data between plated-through holes (PTH) and non plated- through holes (npth) is of fundamental importance!
This means that you must, additional to your Gerber data, output a separate drilling program for pth- and npth drill holes, e.g. as Excellon or Sieb&Meyer data. This applies also to press-fit technology and blind and buried vias in multilayers. ODB++ data contain the necessary information automatically!
Component holes need the accurate hole diamater, vias may have a smaller final diameter due to electroplating (plated through) and PCB surface. Basically, we assume holes < 0,5mm are vias.