granted, that doesn't necessarily correspond to livable space---the things are (rather sensibly) designed to be structurally sound even with all the gravity stuff turned off, and then a lot of the volume is machinery spaces and such, but yes, Craftworlds generally have a floorspace more in common with a planetary surface or three than a typical voidcraft.
Craftworlds, as mentioned, do have such defenses---from truly colossal macro-weapons too large for any lesser voidship, to batteries of more typically sized weapons---but due to their scale, these emplacements are less in the manner of a voidship's weapons batteries and more greatly resemble a planetary-defense fortress built on the vast expanses of their outer hull. Some even maintain strange and exotic engines from before the Fall, whose makings are now beyond the Aeldari, the knowledge of how they were built and the skills and tools for doing so long since perished from the galaxy, but unspeakably deadly when roused to war.
mass-scattering a Craftworld is difficult, yes. Blasting it into a spherical pile of rubble and ruin, on the other hand, is perfectly doable.
It varies. sometimes "destroyed" is "the wards failed, everyone died, and now there's possessed aspect armors shambling around looking for things to kill all over the place." sometimes "destroyed" is "the entire population got wiped out by something or other."
Sometimes it's "Be'lakor suplexed it into the local star."
There's lots of ways to destroy a craftworld, and odds are that by 40k there's at least one of them that were so destroyed.