Repairing siding, old nails
I would certainly think a palm nailer should work. A hammer should also work.

Is it possible that the nails were originally nailed flush but they have released and moved outward? If that is the case, then probably there would be no resistance when tapped lightly with a hammer or even pushed.

If there is resistance, then that would indicate the nails were never driven flush. Probably they were driven with a power nailer set a little too soft.