How can this be? What about her hidden Phylactery... won't she just be able to come back good as new? Or did the adventure specifically state that her Phylactery was found?
The Githyanki Lich-Queen is dead?
Indeed. This is based on the "Incursion" adventure, from Dungeon #[WhatsOrOther] (or was it Dragon? I don't even know). In the adventure, some leatherheads from the Primes trod off to the Astral Plane to counter--you guessed it--an incursion by the githyanki onto their home world. They storm Susurrus, hack apart a lot of githyanki, and then face the Lich-Queen. Obviously, the ending of the adventure depends on whether they successfully defeated Vlaakith and whether they successfully destroyed her phylactery, but we're assuming that both of those happened.
So, she's really dead. Unless you believe those rumors flying out of the Negative Energy Plane that say a shadowy cabal of githyanki necromancers called the Court of Vlaakith is searching for a way to recreate her. Or commune with her spirit. Or produce a simulacrum of her with the nefarious goal of ruling the githyanki with an illusory puppet.
That was Dungeon #100.
She's still officially alive in recent WotC books, but she's dead for Planewalker.com purposes.
Phylactery was found and destroyed for good. She's gone, period. Check out the Rrakkma project forum for some details of the aftermath