My best guess would be that most commercial provider like MarineTraffic wouldn't show those vessels because they would be running duplicate MMSI numbers to hide their identity to make them harder to track.
If you go to marinetraffic.com and look at a military port like San Diego you'll see plenty of military ships (for example https://www.marinetraffic.com/en/ais/home/shipid:5892129/zoo...). Sometimes they spoof, but often they don't, and the trackers show them even when they're spoofing.
