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That is actually a great and very straight-forward question, with an equally great and straight-forward answer. You can generally lay a new roof over the old without any problems as long as:
1) You only have one layer of asphalt shingles on the roof. Most roof frames can support two layers of asphalt shingles, rarely three. Depends on the framing, of course.
2) The shingles lay fairly flat. The new shingles will take on the shape of the old, so if the old shingles are very curled, twisted, or buckled, the new roof will eventually look the same AND the life span of the new shingles may be decreased. This may also void the manufacturer's shingle warranty.
3) There are no existing leaks from undetermined sources. Just putting a new roof over an old roof will not necessarily fix underlying problems, such as with flashing or roof vents. These leaks will most likely recur unless they are properly repaired prior to installation of the new roof.
4) You were satisfied with the performance of the old roof... e.g.. no occasional leaks during rainstorms, etc. This refers back to item (3)... new roof over old roof may not guarantee elimination of leaks.
5) An examination of the roof deck or underlayment shows it to be solid. If there is any widespread warping or softness, repair will necessitate the stripping of old shingles. If the area is large enough, it makes sense to restore the entire roof to new condition.
Ideally, your or your contractor should repair, reseat, or (ideally) replace all flashing around chimneys, valleys, vents, etc. He should also cut off or replace any curling shingles so the new ones lay flat. If you have had ice dam leakage, he should also remove the bottom few feet of old shingles and install an ice and water shield right against the roof sheathing plywood.
You can then be assure that your roof will have a long and healthy life!
It is perfectly normal for roofing nails to extend through the roof plywood, or "sheathing". I am surprised that you didn't notice them from the previous installation. Over time, the moisture in the attic space can cause the bright ends of the new galvanized nails to darken, making them less obvious. If your previous roof was 15 or more years old, that may explain why they seemed to be invisible.
When installing new shingles on your roof, the contractor installed them from the bottom up, so that each successive layer of shingles covered the nails from the lower row. Thus, very few nails are directly exposed to the weather. Good roofing practice requires that any exposed nails be sealed by placing a small amount of roofing cement or silicone caulk under the nail head before setting it. Clear exterior silicone caulk is the obvious choice for a lighter colored roof.
If your new roof was installed over the old roof (up to two layers are permissible provided your roof structure can hold the weight), roofing contractors must use nails that are adequately long to extend through the deck. Though there is consensus as to the shortest nail that is adequate for roofing purposes.... 3d (1 1/4")... it is more typical to find a roofer using a 4d (1 1/2") roofing nail or, in some cases where roofing materials are thicker, a 6d (2") roofing nail. These easily penetrate through two layers of shingles and the sheathing. Your roofer may have opted to use the same nail length throughout. Again, this is perfectly acceptable roofing practice. If you roofer used a nail gun, it is almost guaranteed he used the same nail length for the entire job. It's just easier, more efficient and the difference in cost is minimal compared with the total material's cost. Remember... a roofers TIME is more valuable than the cost of a few longer nails!
In climates that experience extreme wind and rain and/or significant snow, many roofers install a product known as an "ice and water shield" underneath the shingles. This is a self-adhesive, rolled product that is installed directly onto the roof sheathing. It replaces the once commonly-used tarpaper providing a second line of defense against leaks. The advantage of the shield over tarpaper is that it "self-seals" around the nails providing better leak protection than either shingles or a shingle-tar paper combination. This product can be installed over the entire roof if necessary, but is usually installed along the bottom three or six feet of the roof to protect against ice-damming leaks. Also, the use of this product is determined by the slope of the roof and the climate... the more moisture and snow AND the flatter the roof, the more protection the shield can provide!
You are correct... local codes are much more stringent than the national code when it comes to reroofing. The national code does allow two layers of asphalt shingles over an existing layer. In areas with snow loads, though, it is less common to get approval for a third layer... especially heavy-duty 30 year shingles! But the three layer allowance is dependant on an inspection of the roof structure by the local building department to be sure it can carry the weight. So thank you and consider your message passed on!
You would think that ANY scrupulous roofer would let the homeowner know all their options, including the permissible number of layers allowed. But that is my naive-side talking, so ignore me on that count!
There are a few reasons to NOT layer an asphalt roof that should be considered by the homeowner. The first reason is that I have seen many roofs with leaks that reroofing didn't fix! This is usually due to problems with flashing that were not apparent to the roofer. Proper reflashing can require the roofer to do quite a bit of shingle removal and replacement prior to installing the new roof layer, somewhat diminishing the price advantage of layering.
Also, the second roof will not last as long as a new single layer. The primary reason is heat... the hotter the roof gets, the shorter the life of asphalt shingles. Most people would intuitively think this is nutty, especially if they have ever been on a roof. I mean... how much hotter could it get? The truth is... lots! Remember that the temperature of the roof is affected by how well the attic is ventilated. Asphalt roof manufacturers have proven that a cool, well-ventilated attic leads to longer roof life. When you "layer" the roof, the lower layer acts as an insulator so heat does not radiate into the attic space as well as a single layer. Since the upper layer becomes hotter than it would otherwise, the roof's life is measurably shortened. Unfortunately, I have no data to give you regarding the actual reduction in roof life. (If any reader has this information I would be glad to receive it.)
The other factor that may shorten a layered roof's life is the unevenness of the old roof. The new shingles do not lie on a smooth decking... they lie on top of old shingles. This unevenness will eventually reshape the new shingles as they soften with the sun's heat causing them to bend to conform to profile of the old roof. Even the slightest bend is a potential weak spot that may lead to premature breakage... especially if the roof is walked on.
As you can probably tell, I am a one-layer sort of guy. So are the growing numbers of roofers who are tired of callbacks and dissatisfied clients. But I appreciate the additional costs of stripping an old roof. So all I can say is... let the buyer beware!