Stupidity: You would think if the security systems in the computer vault have to be off in order for a technician to access the computer then the computer itself wouldn't be accessible if the security systems were on.
Stupidity: Why, in the most secure computer room you could find, with all those detection devices, did they not install video cameras? There is no risk of a security breach as they could be locked into a position that would not show the computer screen or keyboard but would show that an intruder had entered the room.
Answer: Ethan never thought it was a mole hunt to trap Jim. He found out from Kittridge at the restaurant that it was a mole hunt, but Kittridge believes that Ethan is the mole (the money his parents mysteriously receive). At the station Ethan realises that Jim must be the mole since it is too convenient both he and his wife survived. However, the hunt to catch the mole was never directed at Jim - Kittridge never suspected him until at the end when he sees Jim alive.
swordfish
Actually had suspicions before Jim showed up. Ethan found the Bible that was stamped from the Drake Hotel. Where Jim had literally just come back from before the mission. It made no sense otherwise why that would be in Jim's possession.