This is not normal nor correct. It is common because most people who install roofing systems have no idea what they are doing. The roof deck should be 1 inch or thicker ply wood and the nail should be 3/4 inch nails, with 3/8th inch heads, galvanized and coated. When the nails are driven too deep, they supply a water channel which causes mold to grow on the roof and eventually destroy the whole house. Once the house is infested with mold, you will have to burn it down just to get rid of the mold. That mold could kill your family. Eventually the mold will show outside on the roof and grow under the areas where the nails are penetrating the roof deck. The reason this nail penetration is common is to save the labor of changing the nail pack in the nail gun, and the extra cost of using real roofing nails. It only saves about 100 dollars / house. Some contractors also substitute particle board for plywood which grows mold even faster. Google images for mold on roof.
This is a copy of the code that is about the same in all 50 states. The code states that the nails only penetrate when the roof deck thickness is below 3/4 of an inch. To hold snow, ice, and withstand wind, it has to be at least one inch thick plywood. So if you can see the nail heads and the right nails were used, the roof is too cheap to last anyway. The correct way to do this is with 1 inch or thicker ply wood for the roof deck/sheeting, and 3/4 inch galvanized nails with 3/8th inch heads. Also, the building codes are ridiculously outdated. They should not allow the roof sheeting/decking to be less than one inch or less than 3/4 inches when made of wood, especially in areas with snow.
Fasteners for asphalt shingles shall be galvanized steel, stainless steel, aluminum or copper roofing nails, minimum 12 gage [0.105 inch (3 mm)] shank with a minimum 3/8-inch (10 mm) diameter head, ASTM F 1667, of a length to penetrate through the roofing materials and a minimum of 3/4 inch (19 mm) into the roof sheathing. Where the roof sheathing is less than 3/4 inch (19 mm) thick, the fasteners shall penetrate through the sheathing. Fasteners shall comply with ASTM F 1667.