Can I automatically delete all hidden objects and all unused materials?
Unused materials should disappear from the Materials list automatically. For hidden parts, if you go to the filter on the scene tree, you can select to show only hidden parts, and selectively delete them from there. Be careful though, as it will show groups that have both active and hidden parts, and if you just select all delete, it will delete the group along with the visible parts. Would be nice if that mode would just give a flat view of all the hidden parts so this sort of operation would be a bit simpler.
Thanks mattjgerard. It is really helpful.