It's not exactly what we have now. What I think the article is hinting to is that each of the 162 Natura-2000 areas will be assessed for the impact that aviation might have on these areas. Very sensitive areas will get a Prohibited area (or SRZ, or something to that effect) around them, like the Waddenzee. Less sensitive areas will be marked as a nature reserve with a suggested minimum overfly height, and robust areas will not be marked on the aeronautical maps at all.
Right now virtually none of the 162 areas get any mention on the aeronautical maps or in the AIP.
Nevertheless, nothing (except preliminary discussion) will happen until the appeals process is over.