First of all, those holes are sealed. The bishops tape bonds with the asphalt, making a nice seal under the footer. If they leaked, dish would stop putting them on roofs and I don't wanna hear about the old Frankentech days. (Yeah, I know, there are still some of those around in every office). 2nd, you have other holes in your roof, aside from the thousands of nails, you have chimneys, vents, the ridge vents, which usually only have flashing around them with the shingles over top of them.
You tell 'em, Kat