The provincial highway numbering system evolved over decades, as did probably every municipal road system and just about every other jurisdiction. Trying to clean it up, organize it, or whatever else some folks thinks needs to be done would come with a significant price tag and disruption for questionable benefit.
Fundamentally, 400-series, primary, secondary and tertiary highways are built and maintained to different standards, although there are always exceptions. Plus, there are the connecting links and other roads under provincial jurisdiction that aren't normally publicly number but still have a numerical designation for internal purposes (usually 4-digit). Hwy 11 south of North Bay, although divided, is built to a different standard than Hwy 400 and still has at-grade intersections and private entrances.
Other than 400-series, changing designations on routes where there are addresses would create significant cost and disruption for residents and businesses. Think re-naming Dundas, times lots.