The holes were part of the forming and assembly process. More like locating holes. Yes, they are big, but that makes them actually easier to work with during sheet metal assembly and plug than smaller holes. Of course precision suffered...not that any of us doing some sheet metal work have noticed.
The story I always heard when I worked at dealerships was that those were drain holes. These cars were dipped in water tanks to apply the Electro Deposited Primer and the holes allowed the floor pans to drain.