Never keep your resources in your vault. The legitimate is using your alliance members as banks. By donating resources to a trusted friend who plays in a different time zone, then having them return the resources during the "Server Maintenance Shield" (the 15-minute window where PvP is disabled), you effectively move your wealth outside the reach of raiders.
Below is a report detailing the state of the "War Universe Hack" landscape, focusing on common exploits and their impact on the game's economy. War Universe Hack