Does Hardie require the nail holes to be filled for the warranty to be in effect? I believe it does and that it is in their instructions for the holes to be filled with caulk. Punch list, no BUT should have been filled as the siding was being installed. Unless using the prefinished siding then follow the exact instructions for the finish type.

THis is my info

No, ideally there should not be visible nail holes in a properly installed James Hardie siding. The siding is designed to be blind nailed, meaning the nails are hidden by the course of siding above, according to James Hardie. Face nailing, where nails are visible, is generally not recommended except in specific high-wind situations or as a last resort.If nails are visible, it could indicate an improper installation.

Hardie Plank will almost always need a few face nails because the underlying walls are never perfect. The nails are keeping the bottom of the plank against the plank below so a gap does not show.

They should be caulked prior to paint, or color matched caulk can be used.