Can C3 in the schematic be polarized?
Assuming +Vo is always positive in relation to -Vo, then there is nothing to prevent you using a polarised capacitor. This is indeed the case here.
It doesn't matter how -Vo or +Vo are related to Vin and GND as the converter is isolated, as the input voltages don't affect the rating of the output capacitor.
Your output capacitor should therefore be rated for the output voltage of the DC/DC. For example if you use a 24V output voltage device, then ideally a 30V or higher rated capacitor should be used.
The CY1 and CY2 capacitors are usually very low value (470pF to 2nF) to allow high-frequency noise to have a return path to reduce EMI. They will have no impact on the rating of your output capacitor C3. The voltage rating of the CY* capacitors does matter - it should be at least the 2kV value specified in the datasheet to avoid limiting the isolation voltage rating of the converter.