From my understanding, the government is extremely inefficient technologically (it wouldn't surprise me if most population records are still in paper form and faxed between government departments)
The government inefficiency comes not from the technology, but the complicated rules and ambiguous responsibility between sections.
Note also that the "missing" has different nuance in Japan and in US (I only lived these two countries, so I can only tell about them). In Japan, every resident must register his address to the city or county office; if someone doesn't live in the registered address, the person could be technically "missing" for the purpose of statistics or census (police investigation or other official matter uses more strict definition of "missing", off course.)