A bit more experimentation:
I temporarily connected a laptop to a spare port on the ADSL router (the box at the top of the diagram above). I checked that the Wi-Fi access port on the router was disabled (it was), and I disabled the Wi-Fi connection on the laptop. The only way packets could pass from the laptop to the main network was through the ADSL router, then through the MT1300, and then through the main network switch.
I used socat to set up a constant 100Mbit/sec transfer from my desktop machine (on the main network) to the laptop (connected to the ADSL router). I brought up a network monitor on the laptop. It showed a constant 11.8Mbyte/sec transfer in and about 260kbyte/sec out (presumably ACKs).
I ran tcpdump on the MT1300, specifying any interface of any. It showed a heavy stream of traffic coming into the machine on eth0, but it didn’t show the same traffic being passed on to the laptop.
I installed darkstat, and it didn’t show much traffic passing in either direction.
ip -s a showed heavy traffic through eth0 but no significant traffic through br-wan.
Unplugging either the Wan cable or the Lan cable on the MT1300 caused the data transfer to stop – the value on the laptop’s traffic meter fell to zero. Plugging the cable in quickly enough caused the transfer to resume, because TCP is clever like that. 
Disabling the br-wan port caused (with ip link set br-wan down) caused the transfer to stop.
These two simple tests showed that the traffic was definitely passing through the MT1300, and indeed though the br-wan bridge. So I don’t understand why the traffic doesn’t show up in traffic stats or how to fix it.