I believe LM are trying to get developers to keep files outside of the main P3d folders, hence the reason for removing the Addon Scenery folder. You can easily add it back yourself, but it may be worthwhile putting some where else instead. You'll still need to add scenery.cfg entries anyway, so just point them somewhere outside the main folders instead.
I've set up a separate "P3d user files" folder, and inside that I have Addon Scenery, SimObjects, Effects, Fonts etc and have added the paths to the relevant cfg files. All the 3rd party files have gone in those to keep the main folders clean.