It is crucial that roofing nails of the correct length have been used to secure the shingles. Waterproof sheets that are placed on top of the deck, often called underlayment, need a softer touch. Yes, the subfloor must be held firm, but remember that a layer of shingles will cover it. This is where a hammer stapler stapler is commonly used.
It works fast and the staples are much stronger than a normal office stapler. In cases where you can see that the roof nails go through under the cladding, this is nothing to worry about, as this causes a perfectly fine placement of the roof nails. Roofers often drive nails through the siding, as the roofing nails are impressively long and the materials used for cladding such as plywood or OSB (oriented fiber board) are not as thick, so it is normal for roofing nails to protrude visibly. Surprisingly, roof liners help prevent roof leaks due to the additional layer of planks that adds an additional layer of water protection.
Another common problem with roofing nails is when the pressure is too high in the pneumatic nail gun. If you look at the roof of your attic with a flashlight and can observe the lights passing through the holes in the roof, it's time to renew the roof to prevent water from entering through these holes. If you see dark spots on your ceiling or if you touch a soft spot on your ceiling texture with your hand, then it's a sign that your coating is rotting. A roofing nail should have a nominal 12 gauge minimum shank diameter, 2.67 mm and a minimum head diameter of 9.5 mm.
At the same time, poorly driven nails or what roofers call high nailing cause the air gun to lack pressure to drive the nail and this results in protruding nails. If you are in a workplace when siding is being nailed, you will hear the quick machine-gun-like tat-tat-tat-tat tat of the thousands of nails being driven through the siding as construction workers walk across the roof. Loctite roofing sealant and flashing does the perfect job of sealing roof nails along with other exterior gaps and joints. You would have to replace the tile roof about three times during the life of a metal roof.
Whether or not to nail shingles or shingles directly through the roof sheathing can be very confusing, as improper placement of roof nails will likely lead to leaks and structural damage to the roof. Each of these significantly determines how many nails are needed per board during the installation of the roof lining. Precise nailing affects the performance of roofing shingles and is also required by the International Building Code. That means that although the metal roof will cost you more in the beginning, it will offset the cost in the end.
Roofing nails should go through about a quarter of an inch; I would worry more if they didn't.