Gee, that's a very good question. I can't believe CDC would bypass American-flagged ships. But it's true. This is right off their web site:
"Every vessel that has a foreign itinerary and that carries 13 or more passengers is subject to twice-yearly inspections and, when necessary, to reinspection by the Centers for Disease Control and Prevention (CDC)."
In other words, it's ships with foreign itineraries that they check. Not the Independence or Patriot because they sail in US waters (Hawaii)