If the holes are there the damage is done. You might as well leave them.
I have often noted that I am not a fan of boring holes in decks but most OT's are not historic relics that are damaged by adding them.
I remain committed to tying through the space between the rails and have never seen any rail wear from that.
I do have several boats that have these holes and I never use them for tie-downs during transport. Given that the grain in the decks runs parallel to the decks concentrating the additional stress from a tie down in the center of the deck (not to mention whatever additional stress that comes from wind while driving) is an invitation to further damage the decks. The center of a deck with a hole bored through it is the weakest point between the rails. Putting a knotted rope behind that hole and pulling on it puts all of the stress right in that one spot. You don't need to do a FEA to visualize this. I suppose anyone that has looked at or worked on a lot of canoes has seen their share of the resulting split decks. And, in my opinion, the holes look terrible.
That said, I rarely tie down the front of any of my canoes while they are on the car. I find that the stiffness of a wood hull makes these the extra ties unnecessary. I buy cars that have nice long roof lines (Volvo wagons are ideal) and use good quality Yakima racks, spaced as far apart as possible and cinch down with good quality cinch straps. The only boats I tie in the front is my OT Royalex Penobscott. That boat flexes like crazy in the wind (and in the water).
I don't even tie my 20 footer down in the front. I should note, I don't crawl around on the highway...I do my fair share of passing. Typically I only tie down the bow and stern if I am planning to drive over 2 or 3 hundred miles or if there are real big cross winds.
I have yet to lose or damage a boat (well, there was one about 45 years ago, crappy racks, not well tied, going too fast, sorry Dan)....
Here is a link to another recently recommended "fix" that uses a copper pipe and hole bored through the hull:
http://forums.wcha.org/showthread.php?13937-Painter-s-Rings
Good grief.....