To me scratches are character markings- the main visual difference between a "cottage queen" and a wilderness tripper are the scratches, they prove that you've been in the rough stuff; you've dragged over beaver dams, you put in on gravelly shores, you've painted hidden rocks, and you've dropped it a time or two. None of that happens with cottage boats. Those marks and dings are badges that show you've been a tripper, explorer, and adventurer, and are something to celebrate, not hide. If they're not structural just clean them up and celebrate the memories of the trips where you earned those badges...
All I'd do is fill with some clear epoxy and leave it at that, simply to prevent further "damage" and dirt from collecting, and put it down to experience.