Not positive about it, I think it is in - My Documents/SH3/data/cfg
The file named - "GameplaySettings.cfg"
Last line -
[MiscSettings]
AlwaysAutotargeting=0,3,0,0,0;for warships, merchants, uboats, air and, respectively, land targets
Seems right to me since this new career I have only set the default action for spotting merchants to dive to PD (accidentally

). I haven't set any of the others yet.