Still no update on "Hornblower", but I suspect that the problem is more widespread. In my current test play through "Ardent", I've reached the convoy battle. The enemy ships show up as hostile on my compass, I can shoot at them by auto-aim, I can board them - but they don't shoot back. Worse, one of them surrendered and used the officer's default dialog rather than the usual "Cabinfight_dialog". I couldn't end the quest by capturing or killing him normally; I did manage to kill him by hitting him with a borgiablade, and was not then transferred to the normal ransack screen, instead I was stuck in the ship's cabin.
Attached: all the log files ("error.log" is zipped because it contains a huge list of messages and is too big to upload unzipped!) plus a savegame on worldmap. You're about to be challenged by a French group; decline battle with that, then go to 3D sailing, and you'll be in battle against the convoy.
Strangely, if I reload my old savegame where I'm about to attack the payroll ship, that one does shoot at me. Still needing to be investigated is whether any other storyline quest ships are affected, e.g. Oiseau and Ferro Cerezo's ship in "Tales of a Sea Hawk" or La Couronne and its escorts in "Assassin".
This is with the 28th July install plus 23rd September and "Levis_Fixes_2-10.zip" updates. I probably won't be able to check the 3rd October update until tomorrow evening.