First the evidence that the facility had anything to do with a nuclear programme is pretty thin on the ground. It's actually close to zero, but it makes a good headline. You could find higher than background levels of radiation in many places, particularly tunnels. Ask anyone who lives in Aberdeen and has a cellar
Secondly a substantial underground (tunnel) complex was investigated after the war, so at least some tunnels were known at the time. They comprised one of the sub-plants used in Me 262 production. They have obviously uncovered more of this complex.