At that time, nails and spikes were made of wrought iron. Good wrought iron is more resistant to rust than cast iron, but like all ferrous metals, it rusts. Where nails were used to fasten exposed wood, they were countersunk and the countersinks plugged with wood. Before driving the nail, a strand of marline or oakum, depending upon the size of the nail (or spike) would be wrapped around the nail shank beneath the head and the nail dipped in thick pine tar. This treatment minimized exposure to moisture and thus prevented rusting to some extent. (When done modernly with cut boat nails, this practice is colloquially called "Chinese galvanizing.") Nevertheless, the iron would rust and the nails fail and when tension forces would be applied, a plank would "spring" away from the frame and such "sprung planks" occasioned leaks. For this reason, ships' planking was fastened with "tree nails" ("trunnels") which were wooden pegs tightly driven into bored holes and often wedged at one or both ends. Trunnels were of select wood species and well-dried, so that they would swell even more tightly in place when the vessel was launched and the planking wetted.
Vasa's planking was fastened with trunnels, not iron nails. Her planking was not studded with nails as "decoration."
Of course, this isn't to say that a modeler isn't free to decorate his model however he wishes, but looking at finished kit models is certainly no indication of historic accuracy!