Why exactly does CSM have the tape destroyed? He obviously intends to kill Krycek, after which he will claim that the bomb destroyed the DAT and its carrier. I couldn't figure out why the CSM would destroy the tape without letting the Consortium see it.

After my most recent viewing, I figured it out: the CSM didn't know that Krycek, Cardinal, and the other guy stole the tape from Skinner in the hospital. The CSM was planning on killing Krycek all along and never intended for him to actually come into possession of the tape.

The only thing I noticed besides what's covered in the Guide is why do the super-secret medical files on everybody since 1950 have a fancy door with a keypad inside the Strunghold Mining Facility when there's an old wooden door that appears unprotected outside? This reminds me of the Simpsons ep where Mr. Burns shuts off all the power in Springfield by going through several elaborate passages to access a console and finding a room with a battered screen door with a stray dog wondering in.

Jesse: the CSM didn't know that Krycek, Cardinal, and the other guy stole the tape from Skinner in the hospital.
While you raise an interesting question I don't buy this explanation. CSM wanted to kill two birds with one stone, so to speak for reasons unknown, by eliminating Krycek and the tape together but I doubt he was unaware the trio stole the tape from Skinner. CSM didn't want the Consortium to see it because he lied to them that he had it so by telling them it was destroyed, following the threatening call from Alex, he was relatively safe from the others' wrath for a bit longer.