Yes the rental agency reserves the right to cancel your reservation and perhaps rent you a car at a higher rate.
Whether the agency does this depends on the demand for cars, for example if it is Daytona Week, then central and northern Florida agencies are apt to cancel you.
But if there is a blank in the reservation to fill in your flight number and the flight arrives late, you have a case for having the agency honor the reservation. After all, what good is that blank otherwise? You might have to call the nationwide headquarters of the agency on the spot for help in this regard and they may act as a go between with the agency in whose office you are still standing.