An old saying was "nails are just to hold the parts together until the glue dries." If you don't want to use nails, don't.
That said, the advice on pin nailers is true. They barely need any attention.
I worked in wood for twenty-five years before I got my first nailer. It was a yard sale special and it changed my life and way of working. Now I have framing nailers, coil nailers, a pin nailer, several 16 and 18 gauge brad nailers and at least two staplers. Things that, before, took an hour, were now done in a minute or two.
For nail holes and wax putties, I always keep a jar of white and black around. Not to fill white or black holes, but to alter what the factories offer. A bit of black darkens a batch and a bit of white lightens. I just roll them together. Apply it and, if you don't like the color match, just dig out the previous application and push in the new.
I did a plywood book shelf out of stuff a friend had laying in her yard just to see if I could make something out of it someone would want. Using this wax mixing method, I was able to so closely match the shifts in wood grain colors I couldn't find several of the eighteen gauge nail holes.