The ferries designate a limited number of spaces as reservable. Other spaces are first come-first served for those that drive up without a reservation. The reserving just means you can confirm the time you'll be going and be there for that time. It does not mean the ferry is full, it just means you'll be able to get on a specific ferry if the line-ups are long.
We've arrived early for our reservation and then been able to catch the earlier ferry because there was space. You do not get a refund on your reservation if this happens. This happened when we lived on the Island and were returning home from extended trips through Lower Mainland traffic, which made it difficult to be more precise with our timing.
If someone reserved and doesn't show up, the spot becomes a first come-first served spot. Your reservation is specific for the time/date you booked it.
If you show up late, you become a first come-first served client. There is no priority given to you because you missed your reservation.