The ferry spaces are finite and I'm guessing that if everyone chose to use it there would be queues which would negate the advantage of it being free. Further to this haulage firms will no doubt calculate the speed of passage through London and pay the tolls and pass the cost on to their customers. Lorries containing hazardous chemicals aren't allowed on the ferry so that a certain quantity of commercial traffic is guaranteed to be still using the tunnel crossings.
Traffic coming off the ferry will be mostly routed through the A205 and A206 which are major arterial roads and as capable of handling the traffic as the A102 which now accommodates traffic from both the Silvertown and Blackwall Tunnels.
Also the Rotherhithe Tunnel is still free to use although it is within the congestion charge zone.
The tea they consume is sweet tea which, though delicious, contains diabetes inducing amounts of sugar.