ShortEdged - The picture you have re-posted is of the roof mounted blower for the kitchen hood fan. The only flashing is the integral flange on the blower exterior casing. You can just see the shingle overlaping on the lower right corner. About a 2 inch flange. The roofer said if he had installed this and the other roof vents he would have included I&W shield in those areas for flashing.
But the kitchen hood roof vent was never a problem with regard to leaks.
The leak that came through the roof vent for the bathroom fan was the one that was caused by bad flashing. The water got under at the vent and traveled sideways as it went downwards and was able to find its way behind the shingles due to poor flashing according to the roofer. Caulking the perimeter where the vent meets the shingles on the top and sides, but not bottom, stopped any further leaks at that point.
Again, the roofer did not install these vents. Kudos to him however for addressing the leaks. I am sure he had a nice conversation with the builder about those other subs who hacked his roof install.
The popping nails issue is all the roofers though.
The longer nails in this area, at my guess, are there and were installed by the subs who did the actual installation of the vents. Lazy and used whatever they had on hand to put the roof back together after opening it up to install the vents. Also, the long nails are NOT the ones coming up.
The nails coming up all over the roof are inch and a quarter roofing nails that came off coils from nail guns. (or maybe they were never driven in far enough in the first place......Which was the impression I got from the Rep from the Builder who came out)
I'm not a pro roofer but I would be surprised if any of the nails are actually coming up. My hunch is they were never down. Your sheathing doesn't look bad and those nails hold pretty darn good (from my experience tearing shingles off) unless they happen to hit a seam between the sheathing and that wouldn't happen as frequently as you are seeing. My guess is he had a newbie that didn't adjust his gun right.
Have you kept track to see if any of the nails that have been hammered back down have come up again?