While the center of gravity of the die may be biased slightly toward the 1 side due to holes (and only really matters if the dots are drilled into the surface as opposed to printed), it is unlikely that this effect will be enough to be statistically noticeable. It can also be countered by using a filler in the holes to counter the weight difference if desired. Of more importance are imperfections in the actual shape of the die. For example, corners that are more rounded around a single face will decrease the surface area of that face and make it less likely to end up on the bottom (not because of center of gravity, but because less energy is required to be available during the roll to tip it off of that face ). Also, if the distance between two opposite faces is longer than the others, then those two faces will be less likely to end up on top (or bottom, since one being on the top will make the other the bottom). This last property was used by cheaters, who would sand or shave faces to alter the distance between opposite sides, and is known as shaving the dice.
Mike