Give that man a prize! What you're looking at are small fractures in the fiberglass, most commonly from impacts. Before fiberglass rips or breaks, it can sustain lesser damage, leaving one of these "bruised" spots that's actually a patch of micro-fractures. The resin/cloth matrix has been pushed beyond its ability to stretch or flex (which doesn't take an awful lot). It hasn't lost all of its strength in those little spots, but it's lost some of its original strength.
The good news is that the boat probably isn't in much danger from them and they haven't delaminated, which would usually be indicated by the fracture sitting on top of a cloudy-looking "bubble" where the wood and glass were no longer connected (that would be much more serious). The bad news, is that there is no easy way to make these spots go clear again, aside from cutting them out and installing small patches of new fiberglass. You can sand them a little bit, add some resin and new varnish on top and they will go somewhat clearer, but they aren't going to completely disappear because you can't get the new resin down between the little fibers that make up the fiberglass yarns. As long as they haven't delaminated, most people would just live with them (but do re-varnish the boat on a fairly regular basis to prevent UV from degrading the resin).
There have been strippers built from different wood types, different weights and types of fiberglass, different types and brands of resin and with varying amounts of fiberglassing experience and skill by the builders. All of these things can contribute to how hard you can flex or smack a particular boat before the glass fractures or delaminates, so there isn't really any specific way to minimize this type of damage. Some canoes and some constructions will tend to be more prone to it than others, though as of yet, I haven't ever seen a "damage-proof" stripper..