Really the best thing to do is unbolt the assembly and take a look at the catalyst in each of the converters. You will be able to see very quickly if it is damaged, plugged, or otherwise bad.
When my pre-cat went, it completely self-gutted and there was no catalyst left behind in the converter. It all blew out and clogged up the main cat.
If you have a few dollars to blow on a fancy tool, you can get a cheap camera probe for $20-50 that plus into a USB or phone. Insert that into the oxygen sensor hole, and take a look at the catalyst. That would save you the time and trouble of unbolting the whole assembly.
Only the two pre-cats are monitored by the PCM. Gutting either of these or installing one less active than factory will result in the PCM adjusting fuel/air to accommodate, unless it is otherwise tuned.
Gutting the 3rd cat will not cause any codes, nor will it help nor hinder power. Modern cats are very flow efficient and do not cause backpressure unless they are malfunctioning. Since this one is not monitored, the computer has no way of knowing the state of the catalyst. The only way a 3rd cat issue will cause a code is if it becomes plugged.
Tuner software can indeed disable all of the catalytic converter monitoring and prevent a CEL for gutted cats. As to how this affects fuel/air, it would depend on how the engine was tuned.
For both safety and ethical reasons, I run all three catalytic converters. They don’t hinder the power at all, but significantly reduce carbon monoxide and NOx emissions. This makes it much safer to be around, especially if it is just idling or running slowly with people standing around it. I also live in an urban area, and personally believe it would be unethical to unnecessarily produce NOx and carbon monoxide for the same reasons I find unnecessarily loud exhausts unethical.