In light of this information about when the tapes were destroyed and what they may have contained, I wonder if Mukasey's reluctance to take a stance on waterboarding may have been because he had already been told that he would be facing the issue of the tapes?
Yeah I know it sounds a bit far-fetched, but at the same time the administration could not afford to risk hiring on someone like Mukasey and then have him bite the proverbial hand upon finding out he was embroiled in yet another "missing tapes" controversy. Were I in the WH (and probably why I'm not), I would have given him a very private "top secret" briefing 1:1 (for plausible deniability) that essentially gave him a heads up that he might be having to deal with issues like waterboarding on some taped interrogations and that some of the tapes had been destroyed.
Properly couched, someone like Mukasey - a "true believer" - would probably agree that was just the way things had to be to avoid the "democracy as a suicide pact" that all the "true believers" seem to fear. Of course this makes Mukasey vested in the effort to find no criminality associated with the destruction of the tapes. And that in turn fits with the current behaviour.