That test F-16 with the thousands of microscopic holes was tested, but one serious flaw was that the slightest dirt or obstruction hampered the airflow through those holes. The are just too easy to plug up. Alll those holes had suction, so that the boundary layer was sucked out.
As far as the original holes in spoilers concept goes, I think its because all those holes caused a lot of vortices and eddy currents. Of course, that added tremendous drag.
One good example of such an application was the US Navy Douglas SBD Dauntless, with flaps/dive brakes with holes. It was designed to attack from directly over the target, going into a near vertical dive before releasing the bomb. During the attack/dive phase, it was desirable to keep airspeed as low as possible, hence the application of high drag spoilers.