As per ABYC standards, when a manufacturer builds a boat, foam is supposed to be placed in any voids in the boat not filled by fuel tanks, etc. Many people do aftermarket deck mods without installing foam. As for leaving it open for drainage, if the deck is configured the right way, there's no need to do that, all water will run off the inner deck and go back to the bilge area.
I personally hate the factory deck design of my Triton 1650SC, in fact, everything about the overall boat design sucks. It's like everything they did was an afterthought. Aside from the 'gangsta lean' (boat leans excessively to the right because they've got the console and livewell on the same side) there are plenty of other issues. First, there's a huge hole under the console for dirt and everything else to run into when the deck is washed down, then, in the stern area, they have huge voids all underneath the decking where more crap accumulates. More and more, I miss my little 14' duracraft that I built the inner deck for. That was the easiest boat in the world to keep clean, it took all of about 1 minute to wash down the deck and then clean the tray at the rear bench seat. My Triton takes about 2 hours to get clean, and even then, there's no telling how much crap is still under that inner deck because of their shoddy design.