It doesn’t matter if the government is “honest.” Sooner or later those missing people will be identified by their friends and relatives. There are plenty of conspiracy-oriented websites that would gladly publish the names and other identifying characteristics of every missing person.
The truth, or its semblance, will eventually get known. We will not know the exact number, but we will have an idea.
It’s more than the 100 people the government might be claiming, but it’s probably not 3000 either. It’s somewhere in between.