On the topic of special targets and the Ruhr dams, special target units are removed for the German turn, until they are attacked. Since Chastise has multiple targets, they are all revealed to the Germans (i.e. no longer removed and replaced) once one is attacked. So, they won't appear in the defence minister report.
As for the location of the dams, one option is to mark them on the low altitude daylight map, which I presume won't have an associated cloud bug. Another option would be to use one of our spare unit slots as a 'dam' unit to be placed at the appropriate location (re-create it if destroyed, with a message that ordinary bombs don't do much damage to dams, or something).