No reason at all why the data couldn't be encrypted and queryable anonymously. If you have a specific thing you are looking for, and you think you find it in the data, then get a warrant to find out who you are looking at.
For example the DC sniper. Fine example, that. You query the database for vehicles that were seen in all the locations of the shootings. The system reports a match and you take that to the judge to ask for the person's info to be revealed.
Of course, that isn't how it's being used.
This system has been in place in a city which employs a good friend of mine as a patrol officer. I am told that the system keeps records indefinitely, and that the first thing it was used for when it went online was other officers checking up on where and when their wives had been spotted.