In most places a physician has to sign a death certificate for every death. The physician can either be the attending physician when the patient died during care or a medical examiner otherwise. The death certificate often has a place for "cause of death", and it's the medical examiner who officially designates a homicide. So it's hard (though certainly not impossible) for homicides to disappear from the records entirely.

Here's David Simon (creator of The Wire) explaining how crime stats are 'juked'.

http://www.youtube.com/watch?v=nRt46W3k-qw#t=19m00s

I'll try to paraphrase a key part:

He did acknowledge that while you can use various tricks to hide crime (turn robberies into larcenies), it's very difficult to massage the murder rate numbers since a state medical examiner usually classifies the death.

So how do you bring the murder rate down? They basically instilled a curfew in poorer neighborhoods, and swept the streets every night. Baltimore cops locked up something like a 100,000 people, in a city with about 650,000 people, most never charged with anything.

Definitely check the video out.