The holes, which are only about 1/16 inches in diameter, get filled with epoxy when the boat is glassed. Most people leave the copper stitching in the hole which also helps fill it. They appear as a series of evenly spaced dark specks along the seams.

They are an artifact of the building process which remains in the finished boat, much as staple holes remain in a strip-built boat. (Although there are some who find this offensive too.) But there is nothing wrong with seeing the rivets on an airplane skin or the adz marks on a hand-hewn beam. These things give us more information about the objects they appear on. They tell us how the material was fastened and how it was formed. To me, this is a richer experience than something made out of one piece of molded plastic in the Sharper Image catalog.