Theft on the Rogue is definitely not a problem. Because it's a whitewater run, few canoeists are even seen on the river. Within the permit season it's mostly rafters, and most of them wouldn't be capable of paddling a canoe out if they did try to steal it.
Equipment "loss" can be a problem though. One funny story was an I think in season permit run we did back in the '90s, and not the lodge-to-lodge run as we were camping. One night in an area that is famous for possible bear contacts, we hung our food, but had other kitchen stuff, an empty cooler among them, in camp. The black bears know that coolers contain food, so those are targeted. We had stacked some pots and pans on the cooler to make noise in case we had a "visitation event." We heard the clatter sometime before midnight. I and others got up quickly and chased the bear away. An hour or so later, we heard similar noises from another camp upstream. There are several sites in this area, some close together. The next morning we found out that the enterprising raft crew had anchored one of their rafts out in the river and had all their food in that raft to keep the bears out of it. Well, SURPRISE! Black bears can swim. They have claws and can climb up on rafts. Or at least attempt to. Popped tubes on the raft from bear claw punctures. Live and learn. I don't remember if they actually lost any equipment. Had some extensive patching on the raft to do, of course.
