Personally I don't recall a debate like this before. After a disaster, the number of dead is always something the media wants government to share. Back when I was a county emergency management director, I referred all questions like that to the Medical Examiner for the county. They are not dead until they have a toe tag on them and s/he says they are dead. This should eliminate the up and down fluctuation in the number of deaths. I expect the 1995 Chicago heat wave might have been another time when the cause of death might be more difficult to determine.
Here we have what looks like government trying to diminish the number of deaths from the hurricane. I recall pictures of elderly people in New Orleans, sitting dead in wheelchairs on the street in the aftermath of the disaster. I would think those deaths were counted as being caused by the hurricane, and they were not killed by wind or flooding.
Here is a CNN story where they worked to identify the number of people killed by Hurricane Maria in Puerto Rico, We surveyed 112 Puerto Rican funeral homes to check the accuracy of the hurricane death toll. This is what we found.
This New York Times editorial (shared by Claire Rubin) points to many of the continuing issues — as I've noted before. FEMA is still in response mode, months after the disaster. And this editorial puts a number to the number of Puerto Ricans leaving the island each day at 2,000.