I did some more testing:
I noticed that after some time, the missing LCNs eventually turned up. I eventually realised that this occurred after the OTA EPG grabber had run.
I reset and rescanned my system and opened 2 windows, 1 watching the services and 1 watching the tuner status. As each mux was scanned for the OTA EPG, the missing LCNs appeared.
For a final test, I disabled the OTA EPG module and then reset/rescanned. The LCNs were still missing as expected and did not eventually populate. Next, I streamed 1 channel from a mux with missing LCNs and all of the LCNs for that mux suddenly appeared. This repeated as I streamed other channels from other muxes.