I don't think it makes a whole lot of difference if your lures get scratched or not.  As soon as you use your lure whether casting or trolling they are going to get scratches on them.  Most lures should be fished close to the bottom which means you will hit bottom and therefore rocks.  So protecting your lures and preserving their pristine condition is good for about 5 minutes.  Plus, I have caught plenty of fish on lures that have scratches and paint knocked off.  If you are trolling for lake trout in deep water, you could actually keep your lures pristine for a long time.

As Al Lindner said what is natural about a fill in the blank (Daredevil, silver spoon, jig, Rapala, etc.).  Plus, fishing lures are primarily designed to catch fishermen, if they also catch fish so much the better.  I think structure, water depth, water temperature, time of day, wind, how deep your lure runs and speed of retrieve are much more important than a pristine finish.  It is similar to your canoe, remember when it was new and didn't have any scratches or dents and how proud you were to own it.  Now it has dents and scratches and it works as good as new.