Since ZG and AQ20 have been placed on the map, it seems like they've turned into ghost towns and lost their denizens. Naxx40 long ago flew North, but what other instances (5p or raids) have vanished, and their lore with them?
The only zones that have actually been removed from the game are the old 40 man version of Naxxramas in EPL, and Zul'Gurub. AQ20 now has a 10 person limit, but it's still there and unaltered (You just need to zone in through the portal in a 10 man raid). Naxxramas also lives on, but it's been moved to Northrend, had a bit of a retrofit, and now accommodates 10 or 25 players, and Onyxia's Lair was similarly resized, but not moved and is substantially less changed.
In patch 4.0, Deadmines and Shadowfang Keep were rebuilt from the ground up with new characters, lore, and bosses that continue the stories being told in their respective exterior zones post-cataclysm, and to reflect the changes brought to them in years past by adventurers who have come before.