Adding more layers of polyurethane will not prevent the scratches from showing up in the finish. Whether or not they show up depends simply on the physical hardness of the nails versus the polyurethane: the nails are physically harder, so the polyurethane will generally lose that battle.
Adding a thicker coat can protect THE WOOD better, though. Then only truly deep scratches will make it through the polyurethane finish to damage (gouge) the wood.
As I recall, Aluminum Oxide is the floor finish of preference, now. It provides a stronger, longer lasting, more natural, thinner finish. But it requires more specialized application than polyurethane; it cannot be brushed or rolled on like polyurethane can. Thus, polyurethane remains the do-it-yourself finish of choice.