Clearly...Cirno lost all her genius after she inhaled too much of the red mist in EoSD. That red stuff will mess you up bad.
I think you're on to something here; Reimu, Marisa, and Sakuya all would have inhaled the mist over the course of EoSD, and were also the three human characters unaffected by staring at the moon in IN. Youmu, however, is absent from EoSD, and does in fact go insane after looking at the moon (in what happens to be one of my favorite dialogues in all of Touhou).