I’ll take the other side of Ed’s argument and say hand nailing is best.
Nail guns will either drive the nail too deep (when the air compressor is set too high, hits a “soft” area of the lumber, or driven at a slight angle) or not drive the nail flush (when the air compressor is set too low, the nail hits a knot, or is at the end of a series of nails being driven and the compressor has not “caught up”).
I live in a “high wind” area and nailing is critical. If the nail is driven too deep, the shingle can be sucked off the roof because the nail does not have the proper holding power. If the nail is left slightly too high, the shingle will not lay flat and allow the self-sealing strip to seal.
Air compressors cannot be set perfect for every condition and roofers cannot (will not) check the depth of every nail. Roofers are often paid by the amount of roofing they install per day, not by their quality of nailing.
Hand nailing is better because each nail is carefully looked at because the roofer has to hit it... when nail guns are used, they are looking “forward” to where the next nail is to be installed.
We lay a ruler down to see that nails are driven flush so the self-sealing strip will adhere. We always find many many nails left too high. (As you can imagine, roofers love us...but they don’t argue because they know we’re right.)
Yes, manufacturers allow nail guns and roofers like them. But the argument that you’ll get a sore wrist or they’re a thing of the past isn’t a reason why they’re good or bad.
However, a bigger problem is the nailing not being EXACTLY where they are suppose to nail. Almost all roofers nail too high. This does not allow sufficient strength against blow off. Regardless which you choose, read the wrapper and remind the installer of proper lap, required number of nails and alignment from bottom of EACH shingle.