I am making a crazy guess here, but who thinks the mystery person on the phone with Ted and in the room with Holly, is Xander?! With Nicole back, I could see him taking Holly and keeping her hostage as a way of keeping Nicole as his wife. That would put a wrench in any plans she may have with Eric, until she gets Holly back.
I would expect that all the DiMeras who have lived in the mansion would know about the tunnels. Stefan apparently does not, since he never suggested that the police search there.