Bilateral Air Services Agreement (ASA) – country A sits down with country B and sets limits on what may be flown between the two. Assuming it’s not an Open Skies anything goes deal, the starting point is the size of the local market between country A and country B.
Germany is almost unique in Europe (along with Austria) in collecting true origin/destination data in its national air passenger statistics collection. So they know exactly how many EK passengers are destined for Dubai and how many are travelling onwards. Equally, they know how many passengers are travelling Germany-UAE via other transfer points.
So you can be sure that the rights available under the current bilateral pretty much reflect the true demand for Germany/UAE travel. If Emirates want the additional rights to serve markets beyond DXB, *shrug*. That’s not what’s on the table.