We can still put these people under oath and find out how they destroyed evidence. A pardon keeps you out of jail - NOT out from any accountability.
Yes, they can be subpoenaed to determine the extent of the crimes and if there were any other conspirators, they may be safe from the past crimes but if the lie under oath they will be committing new crimes.
I don't think there is any such thing as a "preemptive" pardon for these people. Either they did the crime, or they didn't. To stand up and say "I need a presidential pardon" means that you did something requiring it. I hope the incoming head of DOJ sees this for what it is, and prosecutes these people accordingly.