This is strictly my opinion, but what you said is my answer-- maybe an old, original-condition canoe should be left as-is, or if not, it's the best starting-place for restoration.
Canoes that I'd leave as-is would be those that show us something we're likely to lose forever if the canoe is changed... even if it's restored with total accuracy. I have in mind a very old Gerrish that was discussed in Wooden Canoe a while back. It was sort of a missing-link between birch barks and wood/canvas canoes.
If I found a 16 foot 1907 Old Town HW, I'd probably want to restore it to period-accuracy and paddle it. Such a canoe isn't likely to be a one-of-a-kind rarity... and paddling a 100 year old canoe is a very cool thing to do. There's a whole lot of history in an old boat... not just the people and events the canoe was involved in, but the times during which the canoe was used. For me, an old canoe is different from an old chair or desk: canoes are used for adventures and in happy times... or to make us happy and more adventurous.
In the realm of antique restoration, a canoe is different too. You don't necessarily take from a canoe's value by stripping and refinishing the interior, the way you might with an old chair or desk. Except, perhaps, with that very old Gerrish. Refinishing comes down to personal preference... and some canoes look wonderful with the old patina-- the answer is one of personal preference.
Canoes are in the same category (to my mind) as old cars: you restore the old model T and get it running and enjoy it.
In the end, "it's your canoe-- do what you want". But, if you find an untouched canoe, you don't have to un-do anything. However, sometimes you run into interesting things that are part of the canoe's history. We have a Detroit with half-ribs that someone added many years ago. Each rib was carefully made and fitted in... a nice job, and although half-ribs were never an option on a Detroit, it's a nice addition. That canoe also has some little copper patches in the planking that are charming... so they'll stay, as part of the history of that canoe. It's always up to you.
There have been discussions here about whether it's okay to put outside stems on a canoe that never had them, or to upgrade a CS Old Town to an AA by trimming in mahogany. Again, "it's your canoe"... and my personal take on that sort of thing is that if the original owner could have ordered the canoe with outside stems or a longer deck, or a different paint color, or whatever... go for it, it's your canoe now.
But, I wouldn't put Old Town's modern seats in an old canoe, or want diamond-head bolts on a pre-1920 model. I like closed gunwales, if they are original to the canoe-- even though they are less practical. I'd rather have a weather-worn original short-deck than a new one. And even though I find planking-patterns fascinating, I prefer a canvas covering to clear fiberglass.
There's a difference between "restoration" and "making usable". The canoe we paddle was "made usable" by someone, but nothing was taken from it that can't be put in order when Denis has time to restore it. Meanwhile, we can paddle it with dogs aboard... and that's a nice option.
By the way, I've never restored a canoe... I just read what others have said here and in books, and look at canoes in-person and in the old catalogs. Can't take credit for the experience that comes from the type of hands-on work of many who post here!