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With a system as advanced as Juiz, I'd imagine the hardware is just as vital as the software. Not to mention for that much data, a digital transfer would probably take longer than a physical one, unless you've got a data pipeline a foot thick. Juiz is probably terabytes big.
As for why #1 didn't seem to notice... dunno, but did they ever say that he'd seen Juiz before then? I think the implication was that he hadn't, and that he was visiting the Neuotech place for the first time, going off to win the game and all. If he didn't know that those holes were supposed to be filled, maybe he figured the data banks were the glowy doohickeys along the walls of the holes, and didn't think too much about it. Especially since he doesn't expect Juiz to disappear. Only thing is, for that theory to work, they had to have gotten those cylinders out before #2 entered the control room (since he was waiting there for them).
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