One more point about all this. In a well-constructed wooden vessel of the eighteenth or nineteenth century (I have no idea about the Santa Maria) there actually would be gaps between the deck and hull planks - sort of.
Shipwrights and naval architects discovered fairly early that it was almost impossible to fit the planks of a big ship together in such a way that they didn’t leak - especially when the ship was working in a seaway. The bending and twisting forces in such circumstances are tremendous, and even the most careful shaping of the boards can’t compensate for them entirely.
Hence the development of caulking. In typical, high-quality work the shipwright would plane off the outside (or, in the case of deck planking top) corners of each plank, either at a slight angle or with a rabbet plane. The result was that a gap, probably somewhere between half and inch and an inch wide, was left on the surface when the planks were spiked into place.
The caulker (a member of a separate, specialist trade) then did his thing. He pounded strands of caulking (usually old rope soaked in hot tar or pitch) tightly into the gap using his caulking irons. (While he was at it, he also stuffed caulk into the counterbored holes over the spikes or treenails that held the planks in place. The counterbores were then filled with wood plugs, which were cut out of the face grain of a board of the same species of wood as the plank.)
The caulking expanded and contracted with changes in the weather; on a hot day it would project a little above the plank, and in cool, dry weather it would be, in plastic modeling terms, countersunk.
I haven’t been on board the Victory in quite a few years, but I know she’s been replanked several times since 1805. (As I recall, only a few of her original components are left.) I suspect that, in view of the price of labor and the fact that she’s never going to go to sea, the modern restorers took some short cuts regarding the planking. (They made plenty of compromises elsewhere. Most of her current spars are made of steel, and her masts are no longer stepped on her keel. They’re steel tubes, and steel rods welded alongside them poke through the bottom of the hull to be embedded in the concrete of the drydock.)
On many models the gaps between the planks are out of scale. One trick that I like, when building a deck from individual wood planks on small scales, is to run a soft pencil around each plank before I install it. The pencil line (which runs all the way through the deck, and will survive any sanding or other brutalization) looks pretty convincingly like a caulked seam.
Again, I’d have to take a good look at that Heller kit before forming an opinion on how best to deal with that particular problem. I’m inclined to think, though, that filling the gaps almost - but not quite- flush with some substance might give just about the right effect.