The holes in the fish hold deck planking are to drain seawater from the catch, into the bilges. This water would find its way through the drainage/limber holes in the frame floors, and would be occasionally pumped out via the deck pump riser.
Just visible at the bottom of the picture is a short removable section of the main deck planking (with two 'finger holes') which was used to sweep any stray fish down into the hold.