It works in other battle types.
I did just open up the pyc file in notepad and noticed that all file path references are to 0.9.8.1 as below
res_mods\0.9.8.1\scripts\client\mods\autoaim_indicator.pyt
This is of course a nonexistant folder as I only have
res_mods\0.9.9\scripts\client\mods\autoaim_indicator.pyt
I have not yet modified the pyt file, but I did copy over all my 9.9 files into a 9.8.1 folder, and am about to go into clanwars now and test to see if it works.
Edit:
Sadly that didn't fix it.