The default behavior of unused GPIOs (it's reset value) is set as input, with an internal switch (NRF_GPIO->PIN_CNF[], bit 1) set to disconnect. This is the recommended configuration of unused GPIOs to ensure that they do not draw current due to floating inputs.
So, just keep the unused pins un-connected on your custom PCB and make sure that these pins have the reset value of NRF_GPIO->PIN_CNF[].
