Unoccupied SMD and TH pads and noise/interference/capacitance
The extra pads, like all parts of a net, will have extra capacitance to surrounding nets.  Whether that matters is hard to tell.  If you have a nearby noise source that will capacitively couple onto your traces and this noise is significant, then it probably will matter.

One way to deal with this is with shielding.  That trades off more capacitance to ground in return for greatly reduced capacitance to the noise source.  If capacitance to ground isn't a issue, then this is a good tradeoff.  One difference to consider between thru hole and SMD pads is that SMD pads are only on one side of the board.  If they are on top, then the bottom layer could possibly be used as a shield, eliminating coupling from noise on the bottom side of the board.  This doesn't work with thru hole pads since they are on both sides of the board.

If the noise source is external to this board, put it in a metal box.  If you are worried about coupling between components on this board, then ground or guard traces may help.