What if the defendant is found not to be guilty? Will the courts return the actual bitcoin, or the value of the bitcoin in USD? If USD, what date/time valuation would they use?
They are seized as a part of a civil forfeiture action, which means that their seizure is completely distinct, and is handled in a separate court with a lower standard of proof ("Preponderance of the evidence" versus "Beyond reasonable doubt"). It's entirely possible that the court finds him not guilty, and yet the civil court handling the forfeiture action finds the forfeiture legal.
In order to get anything returned to him, he would have to contest the forfeiture in a civil court, and essentially the burden of proof would be on him to prove that the coins were not gained through illegal means, which would mean he would have to show where and how he got them.
In the end, the US government measures wealth based on the dollar, so he would be returned whatever was gained when the coins were auctioned off.