By increasing the flow and exposure of air under the liner it will increase the bilge odor. Water gets trapped in the stringer and not all flows to the bilge area but the air that is in contact with this stagnant water will ventilate more freely out of the larger holes. Give credit to the boat designers when they maintain a sealed liner in the bilge and only use small holes to connect compartments. Let me tell you that dry land stinks but we are so used to it that we do not sense it and consider it the standard. Some boats smell more funkier than others depending on the combination of smells, a little spill of diesel fuel, an oil leak, some mold, permeated sanitary hoses and stagnant water plus whatever could be in the trash. The good news is that after three days at sea you should get used to it and not sense any offensive odors.