Don't do it. When bondo gets wet, it swells, and is likely to fall out.
I know of one canoe the owner wanted to get fair as a baby's bottom. Set the tacks and filled each one with bondo. When the canoe was used, the bondo swelled and telegraphed every tack position through the dacron.
You are better off using a little epoxy with a fairing filler (not cab-o-sil or colloidal silica, that stuff won't sand out).
I don't know whether Bondo has branched out from polyester-based fillers to epoxy-based, but you do want epoxy and you don't want polyester. Regular boat epoxy mixed with phenolic microballoons is probably the best bet, mixed thick enough that it stands alone without sagging (it takes a lot higher percentage of balloons than of resin - like 5:1 or better by volume). You will get a better bond if you mix the resin and hardner, stir well, take a small brush and pre-coat the area with a thin, unfilled coat of it and then mix the filler into the rest in the cup. When your filler is ready, fill the pre-coated hole. Since it takes so much filler in the mix to get it thick enough to keep it's shape, it doesn't bond or seal quite as well without the pre-coat of unthickened epoxy.
Dan is right on the money, Bondo does not tolerate water at all and will make a mess, plus it wont adhere to the wood very well at all. And you dont want people calling your canoe the "putty princess"...
I filled old tack holes along planking where ribs had been replaced with thickened epoxy. When it came to sanding the smeared in epoxy, the epoxy is so hard that the wood around the epoxy sanded but not much of the epoxy. Fortunately I had smeared it in pretty smooth so it was not really an issue but I think epoxy can be trouble as a filler. Just remember it doesn't sand all that well.
Would plastic wood filler such as Miracle brand with wood fibre swell like bondo? How forgiving is the canvas after filling showing those tiny dents?
About to canvas my '24 HW and what seemed to be a good planking job now about to be covered for another 83 years, seems a bit lacking in some respects.
Dan, Todd, Andre & Eric - Thanks for the warnings about Bondo. I basically ended up using thickened epoxy using wood flour (very fine sawdust) as a thickener. I dopped the dents with un-thickened epoxy as per Todd's suggestion, then came along and filled with the thickened (loose peanutbutter) stuff. I used a flexible spatula to try and fair the stuff out.
Sanding right now - next step some thinned Linseed oil (RELAX DAN - using mildewcide and treated canvas)
Plain epoxy is most certainly harder than most woods. You would sand a big dish in the cedar long before you managed to level an epoxy-filled hole. Some fillers which you can mix into resin (colodial silica, cotton fiber, chopped glassfibers, talc and most wood flour) leave a cured material which is just as hard, or even harder than, plain resin. These fillers are designed for structural repairs and not for making fairing compounds (plain resin is equally bad as a fairing compound). You need to use a filler that is actually made for fairing as they are far more sandable and fine grained. Most of them are phenolic microballoon-based mixtures which you mix with a small percentage of epoxy resin. When cured, a proper fill using one of these compounds will be similar in hardness to the cedar around it and will sand down quickly, cleenly and level. Epoxy-based fillers stick and seal, last and resist shrinking, swelling or picking up moisture so much better than anything else that it's crazy to mess with hardware store wood fillers - but you need to learn a bit about the various filling mixtures available and pick one designed to do the particular job.