I recently started playing through the Bloodmoon main story line for the first time. When I started The Disapearance of Captain Carius, I found that large sections of Fort Frostmoth's walls are completly missing. I can see through, and walk through them. It is as if the quest actually disabled the walls, and didn't add another type of wall to replace them. There are no Missing nif markers.
This is in version 41.

#1
I am not sure if this is the case but, in Morrowind(I haven'h got into Bloodmoon yet in Morroblivion) when Frostmoth was attacked, it turned into ruins, so some of the wall might have been destroyed as a part of the quest.