I hope the following will be accepted as a constructive suggestion. It's the sort of thing that's relatively easy to fix this early in the project - if you want to - but would be a pain in the derrière later.
In laying a wood deck, each plank is fastened to every beam it crosses. There's a line of nails, or trunnels, running across the deck over every beam.
It's also worth thinking about what those fastenings look like. If they're trunnels, the carpenter starts by boring a hole for each one. He than pounds the trunnel in with a mallet. The top of the trunnel has a slot in it; the carpenter pound a small wood wedge into the slot, expanding the trunnel. Then he hacks the whole thing off flush with an adz. Because the visible part of the trunnel is end grain, it soaks up more of the oil or whatever else is applied to the deck much faster than the face grade n of the surrounding plank does. Another factor: the plank is probably pine and the trunnel is probably locust, which is a darker, harder species. So the trunnel becomes a little darker than the plank - but not a lot.
If the fasteners are iron or copper spikes, the carpenter starts by boring a hole that's a tight fit on the shank of the spike. He then counter bores, with a bigger bit, part way through the plank. He then drives the spike into the hole, so its head winds up slightly below the surface of the plank. In the meantime, somebody else has been using a bung cutter (a hollow drill that's slightly tapered) to cut a bunch of tapered plugs (bungs) out of a pine board. The carpenter dips a bung in caulking compound, and pounds the bung into the hole, covering the head of the spike. When the caulk is dry, he planes tithe protruding bung off flush with the plank.
With that method, what's visible to the eye is a thin, hollow circle, an inch or two in diameter. It's the color of the caulk, probably a slightly brownish black.
Which of those systems was used in the Constitution I'm not sure; Force 9 probably knows. My guess is that pine bungs covered the heads of the copper "bolts" that were supplied by Paul Revere. But maybe she originally had trunnels.
How all this should be represented in 1/96 scale is, of course, up to the individual modeler. But the real deck would have a heck of a lot of fasteners.