Okay, yeah, we are talking about two different detail areas.
I think you're looking at the cavity as a whole, and I believe in the 16' length, the regulations require a certain amount of built in flotation. So one way this can be achieved is to have a sealed off compartment, often foam-filled (or partially foam filled). So if you want to maintain that aspect, you will want to seal the small hole well (deck plates are commonly used as you are on the larger hole, and I think they "count" as being sealed).
What I was referring to is cored panel construction. Thing is, fiberglass is actually a pretty "floppy" material, relative to thickness and weight. So, to make it stiffer, there are a few different techniques. Examples are to make the panel areas smaller, mold in ribs or other features, support with beams, add core, etc.
On a larger flat panel (decks, for example), a cored construction is often used. This uses (if I have the physics right) the tensile strength of a bonded sandwich type panel (sort of like how an I-beam works). Balsa or foam are common core materials. So, you end up with a panel that's around 1/2" to 1" thick (on our size boats) and consists of "bread" that is two skin layers of fiberglass, and "meat" that is balsa or foam core or maybe plywood. These are bonded together with the resin when the boat is built. As long as they stay bonded you have one stiff panel. If they separate, you have three floppy ones (or two floppy and one mushy).
So of course now you have the "opportunity" to get water trapped in the core, which can cause rot, and/or de-bonding. Water can get in via holes (such as fastener holes for hardware) or at edges (like say where you cut for your deck plate IF that area is cored - and it may not be). Builders, unless semi-custom or custom, rarely seal these penetrations very well (if they do it's great).
A more minimal seal would be to paint the edges of exposed core with resin (epoxy, for example). Better is to "reef out" a certain amount of core, paint the new exposed surfaces with plain resin, and then fill back in with thickened epoxy. The latter is sufficient for most places on our boats. (Even more maximum is to close out the core by removing it back further and then bringing the inner skin to meet the outer one with new fiberglass. I did this at the transom drain area on my boat, but did the thickened fill on most areas. There is discussion of the how-to's in a few other threads, and also I believe in Thataway's photo album, Ferret30's album (I think), and maybe in my Sunbeam ~ 22 Cruiser thread.
Now, maybe that area is not even cored!
(However, I'm pretty sure your decks will be, plus the transom and the hull at least up to the V-berth and maybe further.)
Sunbeam