Well, it might be a simple issue of policy or law. They probably are not allow to simply destroy investigation material. For example, in the Acquisition and Procruement Office of the Pentagon, we have to keep the simplest contract for a total of 3 years after it has been closed. I suggest the same thing is at issue here with keeping data long after they are determined to be a non-threat.
I suggest, maybe they record the protests to see if they are 
peaceful. But then again, I haven't fully read the article.
The article notes data being kept on 230 protests after the event, and when they were declared 'not a threat' (“US group exercising constitutional rights.”), i.e. peaceful. Apparently data is also kept on the people and vehicles who attend these protests.
I believe, incidentally, that the reason Able Danger were barred from providing/keeping information on the likes of Atta was regulations against spying on civillians dating back to the Vietnam war era, and the outcry then from spying on peace activists and protestors.
Although it's worth noting from the wikipedia article itself that the evidence of identifying Atta, etc, could just be apocryphal; in particular Curt Weldon (who made the allegation IIRC) has recently restated he is no longer sure that he did in fact see Atta (on a chart; the chart itself also doesn't exist anymore). Pentagon officials (according to the Time report linked in the wikipedia article) deny Atta was ever identified by the group. So it's not a clear cut case as far as I can see; the absence of physical evidence could be either a coverup or simply that there isn't any.
But I have not seen any evidence so far that says, if there was a legal intervention to prevent use of said info (if it existed), that the reason for said legal intervention can be placed in any way upon the then Clinton government.
