This almost sounds as if the state and local governments are upset because they cannot find a legal way of putting the squeeze on live-aboards to bolster their coffers. Some states have made it very expensive to be a live-aboard, charging annual fees that are quite similar to real-estate taxes--even if you're anchored out for more than a predetermined period of time.
Given the current budget crisis, enforcement of the above stated regulation would be next to impossible without someone in the community reporting the information to law enforcement authorities.
I'm relatively confident that most of the problems associated with live-aboards has to do with illegal dumping of raw sewage. This was the case in Solomons, Maryland about 15 years ago when their beautiful harbor area was populated by dozens of sail and power boats every evening. It was a great anchorage because it was easy to hold bottom on a short rode, and it was sheltered from winds in every direction. During the day it buzzed with activities, swimming, crabbing, etc... At night, though, the entire area began smelling like an open sewer. For a brief time anchoring in the harbor area was prohibited. When anchoring was again permitted, law enforcement personnel began checking boats on a regular basis for locks on "Y" valves. The inspections were unannounced and if your "Y" valve was not locked, or worse yet, opened for overboard discharge, you were in serious trouble. The problem quickly abated, Solomons has returned to it's former popularity, and yes, there are some live-aboards there as well.
Maryland has not imposed a live-aboard tax, but it has been proposed several times. I've been told that Virginia has a live-aboard tax, but I have not been able to track down the particulars on this information yet.