Mega -
I don't know that RISA has a recommendation one way or the other on how to handle this. I will say that, during my time working for RISA, we did not generally get many requests for considering reinforcement in the stiffness of beams / columns / walls or slabs. My belief is that in general structural analysis, most engineers are comfortable using the gross section (or some multiple of the gross section) for the equivalent moment of inertia of the concrete element.
Your point about the behavior of concrete slabs being non-isotropic is a good one. The plate element that RISA uses internally is sometimes modified to be orthotropic when it is used in wall elements. But, that is all automated. And, the program never gives the user the ability to unlock orthtropic behavior for plates.
Obviously, if these items are important to you, then you could send a message to the RISA folks and request the feature be added. Though, I have a feeling they would not give that request much priority.... at least not unless a lot of people are requesting it.