You could mount IIC port expanders (Philips PCF8574 or PCF8575) with the relays. If distance is a problem, Philips has a IIC "line driver". This way the processor etc could be located at an "EMI safe" distance and digital signal would only go to the relay box when a switch was required. I do not know what speed you need, but you could run the IIC at a very low frequency and thus become virtually noise free.

Ha' en sjov dag

Erik