most strip builders who use staples do nothing with the holes.  when you glass the boat, the holes are small enough that they fill with epoxy and become like a little small dark dot......that in most cases you really don't notice unless you are looking closely.  if the hull is dark wood, they almost disappear.

some folks who want to make them less visible than they already are will make-up a little putty....wood dust and epoxy... or use a commercial wood putty and fill the holes prior to glassing.  in this approach you may want to experiment a bit on a test strip to ensure that the colour looks right after it is all epoxied.  in most cases, the epoxy will make it darker than it appeared prior to epoxy.

hope that helps....

h

   hspira is right that nothing needs to be done. Mixing a putty with epoxy will leave you with high spots in your sanding. The wood is much softer than the anything mixed with epoxy.

You have two choices, dark holes of light holes. If you wish for light holes use Durham's water putty. It weighs almost nothing when dry because all of the weight is in the water. It also sand about the same as the wood.

   I actually kind of like the way the wire holes look. It shows the process and helps explain it to people when they're drooling over your boat.