ATEX: PCB design for intrinsically safe, output capacitor
The purpose of a properly specified and installed intrinsic safety barrier is to make whatever is on the other side not matter, so you don't need to worry about the capacitor if it's on the non-hazardous side of the barrier. The barrier should very reliably limit energy passed into the hazardous area even if the power supply itself fails in some horrible way. 

Your custom board is going to be installed in the hazardous area so of course it matters.