+1 on Juan de Fuca if you are taking kids. Depends how old and skill levels I guess but I would only take experienced teens on the WCT. I've done the JDF trail as a day trail run. It's very lovely without any of the permitting hassles and much more suitable for a family trip.
Ferry costs and water taxi/ shuttle cost and logistics for the both the WCT and NCT are about equal. So I would not characterize these as hidden costs. There is no permitting fee or hassle for the NCT but the drive is longer, not sure if I would describe it as tedious to a first time visitor…but I would take the drive over the red tape and crowds anytime.
Cape Scott is lovely either way.