Nope, they use core text, same as me. And they do support ligatures, if the font has them. 1ms delay sounds like a reasonable heuristic.
I've never seen Terminal.app use ligatures. I just tested with Lucida Grande, which has ff/ffi/ffl ligatures, and Terminal.app didn't use them at all (it just spaced the characters out on a fixed-width grid). Can you give some examples where Terminal.app will use ligatures?
With regards to the shell prompt, I'm almost positive that Terminal.app is using some heuristic to read the prompt after a <return>. A little experiment with a tunable spinloop and a fake prompt in C suggests that Terminal.app waits for about 1ms after a return character before updating the screen: a delay of 950us produces an "instant" prompt, while a delay of 1050us shows the cursor at the start of the next line. As the article notes, a 1ms delay is not really noticeable, and that kind of delay only has to happen in a handful of situations.