Looking at the PCB specs (I've never had one produced but understand them) I don't think through holes should be 1, assuming they mean plated through holes. I thought all switch holes were plated but one leg of each definitely has to be as half the matrix is on the front of the board where you can't solder...
Pad count - there are 5 holes on the USB traces and 4 grounds on the USB which are the same as switch pins so need to be included in the count, not sure about the screw holes and pads for the controller, diodes and crystal but I would guess they do too.
Unique parts would be 6 (USB socket, crystal, diode, controller, resistor (assuming all three are the same value) and capacitor) unless the 79th one makes an appearance and isn't a duplicate.
Finally on indicators - why not? You don't have to use them but potential buyers may be put off if there are none. JD's point about starting with the GH60 is a good one, shrinking the outer columns and changing the bottom row (controller probably has to move, split space bar) will give you lots of indicators. Could remove the expansion header at the top to save a couple of pennies as it's yet to be used...