First off, there isnt a shingle out there that will last 50 years, its all marketing bullshit, i hope you didnt pay too much for the extended warranty, second, there probably isnt an architectural shingled roof out there that doesnt have a low nail on it. Yeah i know you roofing professionals will say otherwise but i highly doubt it. Also, we just got back from a conference with certain manufacturers and they allow a certain amount of low nails per job. Now how you can determine that x number of low nails is fine but x+1 isnt, i have no idea. The issue is manufacturers are too cheap to make the nailing zone big enough to secure the shingles properly. And like anything, the installers pay the price. We get squeezed from both ends. As for leaking, i dont know where your from but in my part of town, with the underlayments and shingles we use, and the fact that an electro galvanized nail takes like 12 years to start to rust, then god knows how long it takes for the hole to get big enough for the surface tension of water to break enough for there to be a leak. Maybe in 25-30 years you may have a problem, and thats if you dont have caulking on your nails. Caulking probably adds like 8 years to that, and im sorry but there arent many shingles that will last 35 years. Also, you should probably do maintenance on your after the first 10-15 years and every 5-10 years afterwards. Everyone thinks you can just put a roof on and forget about it, a little maintenance can go a long way in the longevity of the roof.