They all do. Water gets trapped in the stringers below the sole and organic particles in salt water decompose and stink. The bilges usually have a false bottom part of the liner but resist the temptation to open up holes as it will mostly help release stronger odors. This water comes from sea spray, rain leaks, wash downs, wet bathing suits and spills. We are talking many gallons. Water trapped usually gets released into the bilge with boat movement. When a boat is used frequently usually the stagnant water gets flushed frequently and stays cleaner. Some disable the pump and fill up the bilge with detergent (hopefully biodegradable) and let it sip back into the hull before flushing out. I'm not a fan of drying the bilge as a small amount of water will help contain odors.
I have a 2004 41. I do not see a false bilge. Lots of limber holes and if you look in the bilge the structural liner is cut back where it joins the real deep bilge area for access to the keel bolts. It looks nothing like some of the older hunters where there truly were places for stuff to ripen and hide.