That's just the way it is. But not to worry. First, cedar doesn't rot readily. Second, the canvas will be stretched on tight, so it's not like pools of water will be oozing around between the canvas and planking. Also, especially during restoration of old hulls, people often treat the exterior with something to decrease water penetration into the planking- drying oil, diluted varnish, etc. Search these forums for threads on treating the exterior.
Potentially worse than water penetration through planking gaps is penetration by sand and other particles. I've restored canoes where the space between canvas and hull was filled with sand, dirt and other debris. Like particles of the filler on the outside of your hull, such debris could hasten wear-through of the canvas. But then on those old canoes I've seen with lots of debris between canvas and planking, the restoration wasn't because of canvas wear-through; it was because of other forms of neglect leading to rot in the ends, decay of the canvas at the gunwales, poor maintenance of interior finish, etc.
Bottom line- prep your hull's exterior to decrease water absorption, canvas well, clean the interior after use, and maintain the varnish. Your canoe and its canvas will last for a long despite the gaps between planks. In fact, some very fine and long-lived historic canoes have such gaps.
Michael