looks like you have two layers of shingles

the first layer with the old gray nails, the second layer with shining nails.  I believe both are 1 1/4 roofing nails, which is a little bit an overkill for the first layer.

 

yes, the nail are supposed to penetrate the wooden deck. Normal installation use about 3 nails per square foot. You have two layers, that means 6 nail per square foot, appears to be in agreement with your photos.