A body shell is constructed using pressed panels that are spot welded, and at various points MIG welded, this means that right from the start of production, the bare steel must have a passive coating, that allows an electrical current to pass through it, but at the same time, repels moisture, so generally, an oil based coating was applied by the steel manufacturer.
Once the body shell was fully constructed, it would need cleaning thoroughly of this coating, this was done by submerging the shell into huge cleansing tanks, and being completely submerged, holes are needed at every point on the shell to allow fluids to flood into inaccessible areas/box sections, and also to allow to drain properly.
The shell would then go on to be electro primer dipped, prior to painting, evidence of this can still be found on any body shell, by looking inside a closed box section, and finding that its coated with primer.
Holes that stop the elements entering the vehicle are then plugged with either metal or plastic grommets, the underside of the shell is then coated with thick rubberised sealer, and then off to be painted
So the holes are a very important part of the construction process, without them you car would have rusted away years ago!
Thom