J.K. Rowling said that the Ministry of Magic had their way of tracking apparition back in a 2000 interview.
Question: How does the wizarding world protect Muggle banks and vaults, etc. from wizards apparating into them and stealing the contents? J.K. Rowling responds: Well, the Ministry of Magic keeps tabs on people apparating. That's why you have to have a license to do it, and the moment you abuse it you can find yourself in serious trouble (or Azkaban!).
So how come the Ministry of Magic aurors and hit wizards do not know that the Death Eater apparition activity had increased after Voldemort's return in Little Hangleton June 1995?