The "reinforced plastic" option, instead of canvas was standard on the 15' "Trapper" and available on the other boats (both clear, under varnish and under painted finishes) at least as far back as about 1970. What's important about this is that it pre-dates most epoxy boatbuilding technology - meaning that the original versions were most likely polyester resin/fiberglass skins. I don't know for sure which resin and which cloth Old Town used, or if they ever actually switched to epoxy resin, but I suspect they all may have been polyester/fiberglass.
Any one-side-fiberglass/one-side-varnished wood construction (even with the best modern epoxy technology) carries some liability when it comes to water absorption. Trapping water which gets in through the varnished areas up against the fiberglass can lead to both discoloration and possibly delamination. It then becomes fairly critical to maintain the varnish well, being pro-active about re-coating any interior dings, cracks or worn spots and also to keep the interior as dry as possible (not a great boat for an afternoon of capsize and recovery practice or sitting right-side-up in the rain).
If the boats were, as I suspect, covered using polyester resin, the vulnerability to water problems increases in a fairly big way. Not only do you have the one-sided glass layer, but you have significantly lower, moisture resistance, bond strength and peel strength compared to epoxy resin. Delamination from both water intrusion and impact is far more likely and there is more chance for staining under the glass.
Repair options: The fiberglass could possibly be removed in problem areas, feathered-out, the wood fixed and new epoxy/fiberglass added and faired-in to fix those areas. This is, however a pretty tricky glassing job and the chances that it will really blend in very well are not great under a clear finish. Areas where the glass has been removed and the wood sanded will be lighter.
Option #2 would be to do the same, but paint the boat, in which case, it will look pretty much like any other wooden Old Town. It should be fully functional with either of these options but, just as when new, it will always be more vulnerable to water intrusion problems and need a little extra care. The canoe below is my '72 Guide and uses this option, although I did the covering myself and used modern epoxy resin.
Option #3 would be to get out the heat gun and strip the glass off, followed by recanvasing. From a long-term durability perspective, this one probably leads the pack, but it may be more work and expense than you and the boat's owner want to get into. If you ever want it to be a 100 year-old canoe, the ability to replace parts more easily, replace canvas as needed and the reduced potential for water problems would be the best bet.