When routing high-speed signals via pads in the board stack-up create parasitic capacitance. Much of the literature recommends removing unused pads except where necessary for routing.
I thought I remembered removing unused pads through the "options", but then having copper (plane or pour) flood based on the copper-to-drill rule. This then caused via pads on some layers to create capacitive coupling that was worse than leaving the pads in play.
Further, there were issues where the accuracy (or inaccuracy) of the drill would be fine if the pad was there. Basically the drill hole placement could "float" within the bounds of the via pad, but that was okay. What was NOT okay was if you removed via pads, then the copper-to-drill would allow the copper to flood closer to the drill such that sometime the drill would go through the copper plane and short out (or at least the "good" board house flagged this as a violation).
I see the "help" on the "Remove unused pads" option says the tool replaces unused pads with anti-pads. Is this how Mentor fixed this issue sometime between PADS 9.5 and PADS VX.1.2?