With the data deleted isn't it like trying to commit someone of murder after the murder weapon mysteriously vanished?
Perhaps even more importantly, if this data gets destroyed and they can't find further evidence to use against the Megaupload bosses, this would mean a federal bureau effectively destroyed a company without having any evidence of them having committed a crime. That would be a very bad thing, and would set a very, very bad precedent.
The reversal by the Supreme Court a few years later was cold comfort to the shell of the company that was left, the 85,000 people it once employed, the partners who lost the value of their holdings in the company, etc.
(And this hysteria lead to Sar-Box, which just happened to be the final nail in the coffin of the traditional IPO startup exit except for a very few massive successes.)