Re: the abandoned tunnels/route across the Hawkesbury River - that is actually the remnants of the original rail bridge and tunnels across the river that had to be replaced in the 1930s. As I understand it the reason for the replacement was that the NSW Government Railways discovered to their horror that one of the bridge pylons had inadvertently been built on top of a giant boulder that was lying in the riverbed, and said boulder had started to wander with the vibrations of the trains running across the bridge, thus the entire structure was becoming increasingly unstable and in serious danger of collapsing.
So a replacement structure was built as quickly as possible, not an easy task in the middle of World War II, with wartime labour and material shortages, while the unstable original bridge was still kept in service out of sheer necesity (with trains restricted to running at greatly reduced speed and to a single track on the 'higher' side).
In any event the new bridge was completed without the original one collapsing, and the line was quickly rerouted across the new structure. Only the original tunnels at each end and the line of stone pylons that once supported the original bridge remain alongside the current bridge. So yeah, they weren't a planned line but an abandoned one.