The roofers used either 7/8" or 1" roofing nails and probably hand nailed the job.
It does not require to penetratr the plank board decking, as long as the penetration into the plank decking is (don’t quote me on this) about 1/2 " to 3/4 inch.
(Dang, now I have to go and look that up. It has faded out of the memory banks.) I will read through my Master Shingle Applicator Manual again.
I say probably hand nailed, because if using a pneumatic nailer, there would be some evidence of the tips of the nails pushing the decking at the bottom, even without complete penetration.
Typically, on plywood decking and oither engineered decking, which are more common, the nails are always noticeable. You are probably used to seeing this the majority of the time.