You don’t have your facts right.
First of all, there were emails in her server, not “documents”, certainly not documents like what Trump had sitting in boxes in a bathroom. None of the emails were marked classified because they were just regular emails and they talked too loosely about classified information.
Second, the destruction of cell phones had nothing to do with evidence. The data is always on the server. As for deleting the server, the FBI couldn’t prove who did that and eventually offered the technician who deleted the server immunity in exchange for complete testimony. The technician said that no one instructed him to delete the server after the subpoena.
The facts just don’t support charges.