Hole diameters in PCB software - finished or tool size?
The easy answer is that you should specify whatever your supplier requires. 

Normal industry practice, in my experience, is to specify finished diameters for both plated and unplated holes. That's certainly what we use in our libraries. If you're using some oddball supplier that requires something different you can always edit the PCB file or the NC drill file  to accommodate them. I'd prefer to have the PCB maker responsible for delivering the boards with holes made right to the specified tolerance, not to tell them to use some drill of specified size that will then cut an oversize hole, that is then plated down by some unknown amount.. 

Note that specifying finished diameters means that plated and unplated holes specified as the same size will generally use different tools.