First of all, the type number of the PLC you mention is not complete (or Omron is using different type numbers in North America and Europe?). There are no expansion units for the CP1 PLC's that can handle encoders. So a second PLC would be an option. You can connect them through the serial ports or ethernet ports (option boards). But the encoder values exchange will be slow. So controlling the stepper drives should be programmed in each PLC separately.
Another option would be remote I/O to hook up the encoders. But that will require more programming. The remote I/O can be connected to the PLC through any option board for serial or ethernet communication.