It's hard to find an exact figure of how many people have been "detained" as material witnesses in what is a thin cover for an unconstitutional arrest. This 2002 article describes how the federal statute has been used:
The Department of Justice has not released an exact tally of persons detained as material witnesses, but it appears that the bulk of detainees who were first detained were brought in as material witnesses. As the investigation continued, many of the "material witnesses" were released or charged with crimes. For example, Osama Awadallah, a student from San Diego, had originally been detained as a material witness after investigators found his name and phone number on a piece of paper in the glove compartment of a hijacker's car. Awadallah told the grand jury that he did not know any of the hijackers, but changed his testimony once he was confronted with evidence that he did know a few of them. Awadallah was charged with perjury and is now being held as a criminal detainee rather than as a material witness. At the time of this report, it appears that only a small portion of the remaining detainees are being held as material witnesses.BTW: I think the Awadallah case is still ongoing. The district court threw out his statements to the grand jury as product of an unconstitutional detention but the 2d Circuit reversed. The latest volley in this battle seems to have been the feds trying to get grand juror's testimony in as to their impression of Mr. Awadallah as he testified (rejected by both the trial and appellate court: sorry can't get a good link but the 2d Cir No. is 05-2566-cr).