When Conestoga Parkway was a self contained short freeway, maybe it made sense to call that one highway (because it was the only one). Now that there is a network of longer freeways, it makes sense to have logical numbering for them all.
408 is the north-south highway from St
Jacobs to Cambridge (401) and maybe eventually to Hamilton Mountain (and the mid-peninsula highway).
477 is the east-west highway from New Hamburg to Guelph, with maybe extension west to Stratford and east to Acton, Georgetown, Bolton, etc.
466 is the north-south highway from Guelph to 401, and maybe eventually Hamilton.
Pretty simple to keep track of.