It was said in T1 that only living matter could go through the time travel process. that is why humans arrive naked. and the terminator has flesh over its skeleton. but in T2, the t1000 is made of pure liquid metal and should not have gotten through.
Since this was at least 14 years later, and they developed a new terminator, they could have corrected the problem of sending a machine through the time portal. We improve on things through years now, so why not in the future?
James Cameron explained (and I believe it was included in the novelization) that the T1000 was made from a form of "living" steel...basically a kind of organic metal. As such, it could go through the time portal.
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