I think I will try this.
God bless me if Skyrim no longer works when I try this.
Then she proberly went to Morthal
Well, it is likely that she was killed by falling rubble. I mean, the sizes of the debris inside the ruins are huge, so it isn't impossible that at least one or two people were caught underneath.
Priest, Vigilants, and other holy people are, according to the dialogue at the end of the quest Touching the sky, protected by their respective gods/goddesses. The only exception was, well, spoilers... (arch curate vyrthur) ... so then she wouldn't be a vampire, but have been killed with the rest of themm, the vamps probobly collapsed the roof on her. The Vigilants at the hall did put up a pretty good fight. Lotsa dead vampires. So I think Isran's rants about them being weak is false. I think they just didn't know what they were up agaist, that the vampires were organized. There are still lots of vigilants around, though.
Its also possible she is in the basement ( but I dont have dawnguard so)
No, actually, there is some Dialogue from when you first walk into Fort Dawnguard. The Vigilant arguing with Isran does confirm that "Carcette is dead."
Also, you can access the cell of the hall of the vigilents afterwards by using the console command coc and then typing in the cell keyword. If you have certain mods, like the build your house anywhere mod, you can even place a door and link it to another door. Meaning, you can recreate a door that gives you access to the actual cell.
That is a 3 year Necrobump there.
Why.