This could not be simpler - don't nail through the shingles!
On a new construction, pre-drywall inspection, I saw something that I see so often.
The siding guys anchored their scaffolding by driving nails through the shingles.
What usually happens is they then "fill" the holes later with caulking or tar.
On this house there were 8 such support arms nailed to the roof. That is a minimum of 16 nail holes.
They did this on my house 19 years ago and my supervisor assured me the holes would be filled and would never leak. Of course they did.
Nailing through shingles exposes holes forever. No caulking or roof tar lasts forever.
The shingles here are new and very pliable.
They can be easily lifted to secure a roof support arm underneath.
Once the job is done the holes can THEN be filled with tar and the shingle laid back down.
This way the holes are permanently filled and protected, and the tar will never let water in.
My recommendation: it's the little stuff that makes big differences! If builders, and subcontractors, pay attention to the little things, it's my experience that that big things will take care of themselves. Care is the first part of the word careful. There are many small reasons to be careful with how things are built. Products and craftsmanship can last a long time if done right!
Jay Markanich Real Estate Inspections, LLC
Based in Bristow, serving all of Northern Virginia.
Office (703) 330-6388 Cell (703) 585-7560