So... really, after all is said and done, for PvE, is targetting any module actually worth it?
Absolutely.
Sub-Targeting is even worth it if the shields are still up, because targeting is generally improved if a sub-target is selected.
Only once the shields are down you start dealing module damage if you hit.
I think weapons with enough piercing always do random module damage along the trajectory, and sub-targeting will allow you to better focus where. However, module damage does not go to the hull and may even delay the kill. (please somebody more knowledgeable confirm or contradict).
Note that the location of modules varies between ships, and chances to hit depend on the angle from where you hit.
Against multiple enemies that interdict me in a row on trading missions I tend to select the Frame Shift Drive to prevent them from leaving and switch to the Power Plant once the FSD is reduced to 0% Health (If I have the. time or need engineering materials). On deadly Anacondas which are currently the most common for me I get very little module damage on the FSD from the front or back, but from the top or bottom it gets reduced quickly. Thats mostly from Pulse Laser turrets, not just Rail Guns (without super penetrator). Once that is gone I switch to the Power Plant to finish faster.
For smaller ships and in Hazardous Resource Extraction Sites I prefer to target the Power Plant, as this makes them simply pop faster.