There are some folks who sell photo etched bolt heads/nuts. For even smaller than those, I dip the end of a toothpick in a puddle of paint the appropriate color and touch lightly to model surface. For instance, a medium gray looks like a flush rivet head on a natural metal finish. The model railroad venders have tiny styrene bolt heads and nuts smaller than any brass threaded fasteners. I try to keep a supply of those on hand.