It is possible that the code to prevent accidental sysnand update was placed in as a function originally intended to be run through a menu icon so that the user could decide when to run it.
When the function started causing bricking issues they may just have removed the menu option and either accidentally or intentionally left the function in.
One can theorize that the code was left in just in case a sysnand update was started which would then trigger the function in ordered to try to block the update. Assuming this is the case, a rare bug could trigger a false positive which activates the function and causes the brick.
This theory should be an easy one to test for someone who has already bricked their console once and successfully repaired it. Just run a system update and if it bricks, we have our culprit. If it doesn't they can just restore and we have eliminated the possibility.
The function could also have simply been left in as dead code though. Programmers do that kind of thing frequently when they are time pressured to release before they are ready. Instead of cleaning up all the code, they just disable it so they don't waste time cleaning up code for the release, knowing full well that they will need to put it back in for the next release. In this case though some rare bug might trigger the function to run anyway even though the programmers believe there is no way the function can be coaxed into running.