Some roofing contractors advertise that they only hand nail shingles.
The argument is that hand nailing of shingles is a better process than
using a pneumatic nailing gun or pneumatic stapler.

Hand Nailing

It is certainly more expensive to hand nail as hand nailing is a more time intensive process. Obviously, the more time it takes to install shingles using hand nailing, the more labor intensive and thus costly the project will be.

Pneumatic Nailing

There are charges associated with using a pneumatic nailer or stapler gun, which include associated hoses and fittings and the air compressor, all which can be expensive. These charges, however, are one time only and the investment is worth the payback due to the savings associated with labor costs.

Summary

Proper placement of nails and proper driving of nails will affect the manufacturers warranty of any shingle. It is important to properly place nails in the shingles in accordance with manufacturers recommendations. It is equally important to ensure that nails are properly driven into the shingles. It all boils down to proper training and techniques of the roofing installer.