Except for special pins, it is possible to keep unused pins open. These pins are set to Hi-Z for input protection (by setting of PDR register) after reset is released. Thus, shoot-through current doesn't flow into these pins even if these pins are left open.
On the other hand, if the pin is connected to GND without a resistor, there is the possibility of a large current flowing into this pin in the case the CPU runs out of control and the pin outputs are changed to high level accidentally. If these pins are not left open, it is recommended to add a pull-up or pull-down resistor.
For more details, refer to RZ/T1 Group User’s Manual: Hardware (R01UH0483) "17.4 Handling of Unused Pins".