That, by itself, should be the kind of thing that should shutdown a company permanently. Remember, this is the aviation industry, where they track the mine where the ore from the bolt was mined, and who tightened the bolt up and with which torque wrench.
Of course if the entire industry is corrupt it doesn't work, but to a certain degree I guess it is robust. This time it led to a potential disaster but it will become safer as a result..
In a normal, healthy situation a company like Boeing should not feel threatened if some problems are exposed from time to time. That is assuming that everybody understand that uncovering these problems is part of the process and is necessary to improve safety and is exactly why and how we have good safety in the first place.
It only becomes a problem when that safety record becomes blemished too much.
I am pretty sure it actually has worked successfully for many decades up until some point, evidenced by consistently improving safety record.
Very likely that number is meaningless. I suspect this is the kind of environment that incentivises hiding non-conformances whenever possible.
For example, better quality control usually results in an increase of number of defects, at least temporarily. But that just because large portion of these defects were undetected before.
So... you are looking at a number that you have nothing to compare to that also depends on how closely the process is monitored and also depends a lot on the definition of what is non-conformance.
It is like trying to give an answer to "what is the length of Britain's coastline?" Everybody knows that you can get whatever answer you want depending on how long the ruler is.