Technically, they are not actually drainage holes - they are there to allow the pannels to line up on the jig when constructing the car (and I belive also to line up the panel when being pressed into shape). BUT they do sort-of work as drainage holes, if the plug is fitted slightly loose and no sealer applied (need to check for rust around the hole / plug quite regular though).
My car had them fitted both sides, never made any difference when mine filled up with water either. Rover had covered the plug tops with that black pitch sound deadening stuff, so were completley sealed off.

Also, the plugs looked like they had been sealed up with seam sealer at the factory - so possibly Rover knew something we don't (increased rust area?).
As for the bodywork, pin-hole size areas will be fine ground back to clean steel and filled over, anything bigger than a 5p coin should really be filled with metal - but if it's not a structural / mounting area (like wings, door skins, bonnet etc) then you could get away with filler for the smaller holes (anything over 2 or 3 inches square would be better off with metal, as filler is likely to flex and crack in larger holes).
SS