I read this question and still have some confusion about it.
If Y capacitor suppresses EMI and we know that the \$ X_c=\frac{1}{2 \pi f C}\$ this means to me that for higher frequencies the capacitive reactance becomes lower. That is to say the Xc becomes higher for lower frequencies.
The EMI here is created by the fast switching of transformers.
How can we simulate this and see this EMI creation and capacitor suppression by simple signal generator, a transformer, a capacitor and maybe with some resistors in SPICE? Can you provide a simplistic diagram? A simple circuit where one can see the effect of the Y capacitor's exitance.