I'm still running stock SH3 with a few non-gameplay-changing mods (planning to install GWX when my career ends), and I find C2 Cargo ships to vary a lot. I've never played with the auto-targeting, but I expect it's pretty accurate and always hits amidships where the periscope/UZO is locked to.
Once you have a torpedo solution and are ready to fire, maybe you can try unlocking the view with 'L', and manually aiming below the bridge before hitting fire. I tend to find that C2s split in two with an almighty bang if I hit there (engine room or fuel bunker). If I hit forward of that point then not a lot happens!
My only suggestion, but I'm hardly a war-weary kaleun yet...
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