For full-size practice, the short answer is "neither".
I'm doubtful of Marquardt's drawing: Curving deck planks to match the shape of the topside is more of a yachting thing, for fancy designs with a king plank down the centreline of the deck. I'm not saying that it was never done. I'm just doubtful.
But if his version was to be produced in a ship, the planks could not be edge-bent in practice. Forcing such substantial pieces to bend in their wider dimension, without twisting along their length, might be possible but it would be a huge headache. Meanwhile, cutting planks from wide stock is not only massively wasteful, it also leaves a lot of cross-grain and hence unacceptable weakness in the hull of a real vessel (as distinct from a static model). That's OK in small lapstrake boats but not in shipbuilding.
Of course, the shipwright would spile, in the sense of measuring and laying off the curved shape required. He would then look through his pile of sawn plank for a piece with "sny" (a grown curve in the plank and its grain) that roughly matched the required shape, and would make the piece he needed from that.
I went looking for images of windlasses similar to my previous guess and found a couple that had been sold in recent years but were still posted on he sale websites -- both once-lovely bronze yacht fittings, as those are the ones that have survived:
If you are trying to represent the treenails of full-size vessels, those are about an inch or inch-and-a-half in diameter, so a bit less than 1/32 at 1:50. That would be close enough to be going on with though.
I would be very surprised if there is any contemporary written information on the deck planks of Elizabethan ships. (There was very, very little written about any English ship structures before 1700.) There may be good archaeological data, much of it from study of the Gresham Ship. I ought to get a copy of the report on that work but I don't have access to it so I can't confirm what they may have found. There may be more detail from the Mary Rose, though she was a generation earlier. (I do have 3 volumes of her report but not the one on ship structure! Back in the day, the publisher failed to fulfil my standing order.)
For what it's worth, the contemporary Basque whaler excavated at Red Bay, Labrador (for which I have the full report) had deck planking of 25 to 35 cm width and 3 to 4 cm thickness. None survived in its recognizable position from the upper decks but dimensions could be deduced from fastening holes in the beams and the thickness of other pieces that the planking butted up against. At 1:60, 0.5mm thickness and 5mm width would be about right for the decks visible in a model.
The outer planking of that ship was white oak, as were the structural parts, but wood fragments interpreted as remnants of planking from the upper decks included pine and larch. I don't think that the archaeologists' report drew the conclusion but I'll guess that the upper-deck planking had not survived because it was (less durable) softwood. If so, the colour should be about the same as in the holystoned pine deck of a 19th Century Yankee clipper.
That being said, please take note of the variable plank widths on the whaler. Whatever else, she did not have evenly laid, parallel-sided deck planking. I'll add another guess based on other evidence from her time: Much of the visible "deck" probably wasn't planked at all but was one long opening, mostly covered by gratings, running down the centreline, with planking only on what we might call "side-decks". In short, reproducing the appearance of the real Golden Hind, as seen from above, would need a lot of study followed by some sweeping assumptions. If you're not looking at going that far, then there may not be much point in worrying excessively about plank widths and colours.
Kenchington's post in Edge-set deck planking was marked as the answer