Also 9.0.2 with a 6s. Just done a restore from 2 previous backups on iCloud and no luck. Still no 3D Touch shortcuts with mail, music and FaceTime. I waited for the full restore to be completed. All other apps work fine. My only option has to been to erase all content and set up as a new phone. Bit annoying but seems the only solution.
Although I have found a new problem where I am unable to swap any apps from the dock at the bottom of the screen? Is that another bug in 9.0.2?