It shouldn't be possible to lower your the EVs in one special stat but not the other as they are tied together, the same way it's already implemented for the DVs. To
quote Bulbapedia: "EVs behave the same in Generation II as they did in Generation I. Both Special Attack and Special Defense share the EV for Special to maintain compatibility. "
This matters for a few competetively relevant situations like the following:
1. Lowering the special defense on Mirror Coar Smeargle to ensure you OHKO Thunderbolt Raikou would have worse synergy with special attacks like Sacred Fire.
2. Lowering the special attack on Dragon Breath Steelix so that Leftovers heals all the damage a Zapdos takes from it, not allowing it to Rest the paralysis off, would not be a viable strategy anymore as the loss of special defense would not be worth it.