I haven't used them with boats, but back in my relative youth my outing club used mechanical ascenders (and prussiks) for alpine mountaineering and vertical caving. We learned to set up z-drags in glacier crevasse rescue and mountain evacuation practice. I also worked at the time selling gear in the local independent wilderness outfitter store where we salespeople got vendor training in the dos and don'ts of various pieces of gear. General consensus was that safest mechanical ascenders to use on muddy, wet or icey ropes were Gibbs. Mountaineers at the time typically used jumars since they were easier to handle with gloves on, but after some high-profile accidents due to failure many that I knew switched to the Gibbs.
I think concerns about rope wear are overstated -- it's one thing to be worried about sheath wear with a climbing rope that has to take thousands of pounds of dynamic force load in a leader fall. The stress that would be placed by even the heaviest canoe on a rope is minimal (unless you are dropping it in a free fall off a cliff). If one is using competent cordage (not hardware store clothesline) the effect of the cams in a mechanical ascender would be negligible. BTW, Gibbs don't have teeth like other ascenders do, so they are less damaging anyway.
I always found prussiks to be a PITA -- the only benefit to them is they are more portable than a mechanical ascender and could be used for other purposes on a trip.
Gibbs ascenders are amazing little devices. I once climbed a 230' free dropped rope (under a highway bridge) using two of them on a chest and foot strap harness and helped with rescue evacuations where we used them to manage descent with a Stokes litter. I used to always carry one with me on any wilderness trip.
But, surprisingly, it seems like rescue pros are going back to prussiks for some use. To wit, an article on prussiks vs. Gibbs on an "adventure rope gear" site:
Pull-Up Strap Handle Kit
Kayak & Canoe Covers
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