The deck should be sealed so water drains overboard and not into the bilge where it has to be evacuated. The deck ports are inspection ports, these should not allow water to penetrate.
While stored and not exposed to the elements (boat is covered or stored out of the weather), slotted covers may allow the bilge to breath better, but it isn't a sealed environment. GW usually uses rubber between the braces and tank, which it appears from your picture, you have. If you store out of the weather, the slotted covers look like an option. If it were me, I'd position the boat so the bilge drains out the garboard plug, pull the deck every couple of years, spray the area with a mildew remover and cleaner (I like the Zep in the blue gallon container sold at HD). Let is sit a few minutes and hose it all out. Then install the deck, reseal with GE Silicone (almond) and inspect the inspection ports. You can buy rubber rings or replace entirely from Beckson Marine. I don't think there is a method to get the bilge to breath. I wouldn't worry about the wood being wet. It if deteriorates, it is simple bracing for the deck that can be replaced. Just my 2 pennies.
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