The rule actually says that it "should not be held lower than the withers, not May NOT be. It is about midway through the faults listed in order of severity. If a judge is faced with a class full of low necked horses (because breeders started to breed them that way), then the judge has to place them as this is not a fault that allows for elimination.
I seem to recall a rule about eliminating horses that hold their head so low that their ear is lower than their poll for more than four strides, but I don’t think that was kept as a rule (but I may be wrong)