The WTF folder itself is still there, but the content of the addon SavedVariables files in the WTF folder isn't.
Essentially, when the WoW client closes, it goes through a list of global variables addons have registered as containing their settings and writes them to disk. This issue happens if:
- The stored variable content has not yet been (fully) loaded when the client closes (crash during loading screen) - the "client exiting" code still runs, but the variables are empty. Thus, the client writes "empty variable" into all configuration files. This usually causes the entire UI to be reset to default configurations
- The client was in the process of replacing old stored data with new stored data and crashes right after wiping the old data but before (fully) writing the new data; this usually causes a single addon's configuration to disappear/be broken