Here is what I can offer about treenails, based on an apprenticeship as a wooden shipwright and forty years excavating and recording wooden ships from the Bronze Age up to the 20th century. Currently, I am responsible for Vasa, the Swedish warship of 1628.
1. Treenails were the most common method of attaching planks to frames from Viking times up to the 19th century in all of the northern European shipbuilding traditions, until iron production was sufficiently industrialized to make nails/spikes an affordable option. There are exceptions, but generally, nails were only used at the butts or tips of scarfs on all of the ships I have seen from before 1800. Deck planks could be attached by either nails or treenails. If nails are used, they may be countersunk and covered by wooden bungs, but not always. Nails vs treenails for deck planks does not seem to show any consistent pattern that I have seen - Vasa has the deck planks nailed down, without bungs, while the B71 ferry of about the same period and construction tradition has the deck planks fastened with treenails.
2. Planks are almost never fastened to frames or beams with a single treenail. They are almost always fastened with at least two treenails (or nails), one near each edge, and wider planks can have three or even four fasteners. There is a general tendency to stagger these fastenings, although the pattern is rarely absolutely regular, and I have seen plenty of cases where the treenails or other fastenings are in a line.
3. The smallest treenails I have seen for planks to frames are about 20 mm (3/4 inch), on boats in the range of 10-15 m (35-50 feet) long. The largest treenails I have seen are about 35 mm (1 3/8 inch) on big ships over 40 m (140 feet) long, but I have also seen treenails that size on 17th-century Dutch vessels less than 20 m (66 feet) long. 28-32 mm (1 1/8 to 1 1/4 inch) seems to be a very common size across a wide range of vessel sizes for ships built in oak from the Middle Ages onward.
4. Treenails have the end grain exposed, which tends to be darker than the surrounding long grain of the plank, even if of the same species, so in dry wood they can stand out, but what one sees is the difference in texture and color, not the outline of the edge. Once the wood gets wet, a lot of that difference disappears, and treenails become devilishly difficult to find, even when looking for them in full-sized timbers.
5. Bungs can be cut either with the end grain or the long grain exposed (I have seen both on real ships), but there is a general tendency to cut them with the long grain exposed, and an effort made to orient the grain of the bung with the grain of the surrounding plank. They effectively disappear.
6. Metal fastenings are iron, except in some very high-end state-built ships after 1650 or so, like HMS Victory, until copper alloy becomes a little more common on some merchant vessels in the 19th century for a few key fastenings. Even in Sweden, which produced most of the world's copper until the 18th century and where it was comparatively cheap, ships were fastened with iron (bronze costs about eight times what iron costs).
7. As was noted in a post above, interior furnishings are more likely to be held in place with nails than treenails or pegs. This does not include ceiling, as many of the main shipbuilding traditions in northern Europe tried to connect the ceiling, frames and planking with treenails which went through all three layers. This was especially typical of Dutch construction, in which the ceiling tends to be the same thickness as the planking and is a major strength member.
8. Some shipbuilders follow published specifications relatively closely, such as British and French naval yards run by the state, but many more do not. Merchant ships show a wide variation in practice, even within the same region, and I have looked at plenty of ships with variations within the same ship.
The bottom line is that reality is a lot messier than either contemporary treatises or modern modellers' handbooks would lead you to believe. And before someone says that "archaeology only shows us the ships that failed," I will note that a large number of the ships we have to look at are not wrecks, but ships which served long careers and were then abandoned or deliberately buried as cribbing. There is no difference that I can see in the fastening practice.
Fred Hocker