A pinch in a wire would probably kill the battery faster. This is likely to be electronics problem somewhere down the line. In the shifters or derailleurs. Or junction boxes? Are they simple splice points or do they have electronics components? I never looked inside them.

To have a functional system, which drains battery 100 times faster than normal, now that's unusual. This would indicate the problem is low impedance (almost but not quite a "short") between - and + Wild guess: electrolytic capacitor. Not that it matters a whole lot. You aren't going to be fixing this to electronic component level. Disconnect each part of the system in turn until battery stops draining. That's your problem. Replace the entire part.

When we troubleshoot this for reals, we'd use a multi-meter to check current draw of each component, and use a FLIR to see which component is heating. Lots of power draw has to cause heating somewhere.

have your shop use the shimano diagnostic tool. it will tell you, at lease, where the problem is coming from

Nope, already tried it. It says no errors.

I had a similar issue with my DI2 9000 system. Checked cables, changed out junction box and changed batteries. turned out to be the battery mount (short external mt). Once I did that I had no more problems. I have the diagnostic tool and it didn't diagnose the fault. i tried the batt mt after a suggestion from Shimano USA.