This is a deep DEEP problem and one I've been watching for many years. Since about 1993 in fact. There is quite a connection between missing children, Child Protective Services, family court AND the welfare agencies. At least in the one state where I worked.
What I have concluded is that many of these "missing children" were in families that qualified for public assistance. In my thinking, this is because these are the families that have the least ability to afford lawyers, investigators and money to fight the system and to EXPOSE the system.
There are children in foster care that have simply disappeared, (case records and all). So it stands to reason that those sitting in these "perceived" seats of power will simply alter the statistics and remove what is necessary to save face (and prosecution).
The high number of missing children will add funding to continue their supposed "high value" work pretending to search for these same missing children. But when it all plays out, they have received their federal dollars and they are starting to be exposed as potential "exploiters of children" they simply shift gears and downsize the statistics accordingly.
If this process was all above board you can bet your life on it that it would be all over the news about how great the work they've done in finding these "lost" children because this would show the "need" in continuing their efforts and the "need" for more funding to do their "excellent" work. Would be interesting to see their response to a FOIA request wouldn't it?