Apparently Karliah goes different places for different people after the thieves guild questline is over. For me she went to the basemant of the bar in Winterhold, but for some, she goes back to Snow Veil Sanctum where the cinematic occurred with Mercer Frey. Either way, she says she's supposed to go to Nightingale Hall, but she never does. Also, Nocturnal said something about a portal that would open up if her lair was being attacked or something...well, that never happens.
It seems to me like the thieves guild was very rushed by the developers and seems utterly incomplete.
Maybe she only reappears if the quest line is over (including the guild master).
I just now finished getting all the stuff to become guild master, and Karliah was at my ceremony, so maybe she's out and about in the world again now. I'll let you know if she turns up in one of the places I've looked before.