IIRC, small task forces are less suseptible to being spotted, but if they are spotted, they'll still get hammered. Might be a moot point when considering the end result (in many cases), but don't think that a small trans/cargo/oiler TF won't get attacked.
I also believe the Japanese sub doctrine doesn't exclude APs/etc from being attacked, only that J subs will target combatants if the AI has its druthers.