The other use putting those holes in would be if items were being sold at a reduced price - it would prevent them being brought back with a receipt from a full priced game. This was done with books, records, cds, dvds what not. Records would sometimes have the corners cut off. Items so marked were usually called cut-outs or overstocks. Back in the good old days it was not uncommon to see records for $1 or $.50in the cut out bins when regular items would cost $8 or so. For people who were into music those bins were a bonanza since a lot of good (and obscure) stuff wound up in those bins.
This was done to help retailers since they usually provided receipts that didn't specify each purchase by title -just what category it feil in.
*This is still done with books - usually they mark the page sides of the book with a magic marker.