My experience jives with the OP.
I'm terrible at aiming. I'm a lefty so my flight controls are limited. I'm not complaining, as I do real well using joy+keyboard combo to maneuver.
That said, I have all my joystick buttons used up. I don't have a secondary fire available on it so I mapped a key close to my keyboard arrows.
When I tried the C2 Imperial hammer railgun I was sorely disappointed. I was able to hit the hull of my target but could never hit the powerplant.
Nevertheless, the damage was minimal. So I switched to C2 gimbaled cannon. When I hit the power plant with those, it took it down 25% or more.