As one who hand-nailed the first 14 years, then used a nail gun on the last 9 years, I have to say that although hand nailing is better in some respects, such as the ability to have perfect control over the nail every time, it just takes to dang long. Nail guns are a fact of life these days in construction. I found I HAD to start using nail guns just to stay competitive. And now, I use them for EVERYTHING including shingles, deck staplers for shakes, palm nailers for those tight spaces, felt nailers for underlayments, and framing gun for redecking. They're great.
Just keep in mind that you have to stay on top of the gun, depending on how cold it is outside, how warm the shingles, are, how hard the wood is, etc. There is a hazard of "blowing through" the shingles, or not setting the nail flush. Keep a hammer next to you so you can hammer down any nails which stick up a bit, and turn down gun pressure if nails start to blow through.
And forget about using a staple gun for asphalt shingles. They don't hold the shingles in wind very well, and are outlawed in many localities.
And lastly, be very carefull, They provide goggles with nail guns for a reason.