The number of illnesses tested for varies by state, but yes, ultimately NPIP certified is not a "Clean Bill of Health", even on the date inspected. Like "organic", "low fat", and a number of other terms of art, the words have very specific definitions which often bear little resemblance to what...
Washington's Dept of AG site on NPIP
$85 / hour when the Feds aren't footing the bill. (No idea if they are or not right now). A small flock and a good set up, total time should be under 2 hours.
As others have said. FL is free, they test for AI and Pullorum. Its not a guarantee of anything else. It does mean that they tested free of those things, at the time they were tested. FL tests twice a year, but they only do one of the tests annually - so it may be that the flock tested clean...