Update for anyone else who may come across this post in the future, or Woodsmit if still relevant for you:

When returning to NCE before opening hours, it's really simple. Just follow the signs for the central car rental location. Pull up to the double gate and it'll open automatically. Find the SIXT (or any other brand)-specific line. Park car, lock it, and then drop the keys in the orange box that says SIXT. All the companies have a drop box along the line facing you when you pull in. If it's before opening hours I always suggest doing a video walkaround and/or taking photos of the car to document as-returned damages as well.

As an aside I suggest filling the car up the night before if possible, as the on-airport gas station was closed at 3AM despite the 24h sign on the billboard.