Is hand-nailing better than using nail guns?
Yes, for a variety of reasons. Many roofing contractors, especially in Texas(where as nearly all contractors) hire sub-contracted crews. This means the crew is financially incentivized to get off your roof as fast as they can so they can move onto to the next job.
What does this mean for you? This means overdriven, underdriven, mis-driven, and misplaced nails which void your shingle manufacturers warranty!
The graphic below is from GAF's warranty manual that states if the nail does not look like the flat flush nail head on the left, you will not have manufacturers warranty coverage.
This is an example of an overdriven nail. A very common find on roofs that were installed with coil nail guns. Once the tar strip wears out, which is usually 7-8 years after the roof install, you'll be relying on the quality of the installation to keep your roof from blowing off.
Nail guns aren't inherently bad.. Kinda like socialism. It's the inevitable mis-use of the nail guns. Nails are being shot out at over 900 mph with varying pressure with each pull of the trigger or bump fire. There is no way to make sure every nail is perfect unless it's driven with a hatchet/hammer. Good Guys Roofing is one of the premier roofing contractors in the Dallas and Fort Worth area (DFW) and they install asphalt shingle roofs with hammers.
Below is photo from a Good Guys Roofing install. When you hire Good Guys Roofing to install your roof with hammers, you'll have shingles that look like this. Notice every nail is perfectly flat and flush within the common bond area of the shingle below it ensuring you'll never have a blow-off.