"The hard drive is gone" scene contains an obviously missing motherboard in that computer case with some power cables sticking out of the place where normally motherboard back plate is. That does not necessarily mean that the HDD is gone. It can still be inside the case and pretty intact. Connect it to any working PC and you're done! You can't actually see the hard drive being gone or not from that angle even if the case was open.
The first time Castle and Beckett go to Dial A Goddess, Beckett kicks the door in because she hears a woman saying things like 'stop, you're hurting me,' getting progressively louder. Once they enter the office, those sounds have suddenly stopped, with no indication where they were coming from.
When he leaves a meeting with Castle, Mr. Smith uses a chess metaphor that a well-placed pawn is more powerful than a king. Although it's the most important piece, and its capture the ultimate goal, the king actually has little real power within the game. If Mr. Smith knows the game well enough to use the metaphor, he would know that and wouldn't have used it in the first place.