Nicolas,
Drilling a lot of holes may cause the plate to warp. Holes under the rails should not be a problem since the rails act as a stiffener when bolted
to the plate. If you drill addtional holes between the rails for weight reduction that is where you are most likely to get warpage.
Holes between the rails should be done in the center of the plate and arranged so that you have the equivilant of x patterns in the plate
about the holes.
Before you anything, maybe you want to see just how much weight reduction you are getting since it may not be worth doing in the first place.
RICH