For seeing through illusions, I think the best approach may be to decide who can identify illusions, and that will help you decide how they do it.
My first thoughts are that anyone could conceivably identify an illusion, but it requires a special effect to see through an illusion. Let's see if I can explain that a bit better.
A Soshi shugenja creates a compartment in the wall of his bedroom, hiding blackmail material in it. They then cast an illusion over it, to make it seem like a completely untouched wall. When a particularly astute magistrate comes to search the room, for whatever reason, they might be able to identify that there's something weird about that wall. To see exactly what's behind it would require either a spell, a spirit or maybe the abilities of a Technique (Kitsuki, I'm looking at you).
Gut instinct, taking enough raises on your Investigation roll to search an area would let you identify an illusion.