Iirc the MkV carrier is nuke-immune, and all carriers are only partially affected by emps (it stops their movement and their firing, but not their unloading; I think).
But lower-mark carriers can be nuked and, iirc, it will destroy the carrier and anything inside the carrier that was not nuke immune.
Someone may have more recent experience with this than I do, though. Much of the above was changed (sometimes multiple times) since 7.0.