Had a high-end Miyata roadster with such holes. Old-style fixed-and-adjustable-cup bottom brackets were much more susceptible to moisture than are modern sealed units. At best, they had that little plastic cover over the spindle.
Moisture can condense inside frame tubes, and these drain holes would let accumulated water either drain or evaporate.
They were never common, to my knowledge, so there must not have been a consensus that they were a good idea.