I didn't know anyone was still hand nailing shingles! Yes, hand nailed
is supposedly better. More precise placement---on the arch. shingles,
the nail should go through the lower part of the shingle that has
multiple layers. Too low, and it winds up showing which could result
in a leak. Also, gun nails are more likely to be overdriven, breaking
through the shingle and losing the function of that nail, or
underdriven, which can inhibit the sealing of the shingle (shingles
have adhesive strips which sort of glue the layers together to prevent
the wind from flapping up a shingle). That said, I think a decent
roofer with a decent gun will not be so sloppy that it will be a
problem. And I'd guess the problem that roofer 2 is worried about is
gaps in the decking. If this was the case, roofer 1 would have to deal
with it too. Provided roofer two is reputable, I'd go with him.