Good question. There's no good technical info on the GiTS film available in the U.S., as far as I'm aware. In any case, the name "thermoptic" implies infrared and optical camo (that's how I see it, at least) so I imagine the T-X wouldn't have trouble detecting Kusanagi (based on your information).The T-X would likely be equipped with at least equivalent and probably superior sensors.
What was the tank equipped with?
Motoko Aramaki (a more powerful version of Kusanagi) can hack into government databases (not instantaneously, however), and heavily-encrypted cyberbrains within a matter of seconds. However, the T-X is not connected to any sort of network, as you point out, so she would probably have to establish a physical link with the T-X (something the T-X is going to be less than willing to allow to happen).Terminator brains use the same technology, but on a smaller scale. They have natural language ability (T2 An Evil Hour, Russel Blackford.) and can hack thorugh the Los Angeles 'secured' school records database in under a second. In comparison, hacking through modern encryption with modern computers, does as I am sure you know, take a very long time.
Motoko could possibly win would be if she transported to another body and returned with adequate weaponry, but even then I would still favor the T-X.
BTW, Motoko is the protagonist from the Ghost in the Shell anime/manga franchise (not a wankverse).