Is it harmful to write to unused bits in PORT registers?
If the pins have no connection to the outside world (i.e., they don't have any actual pin associated with them on the SAM3X chip) then writing to the PORT (or indeed any other register associated with them) will have no effect whatsoever.

If they have a pin but that pin is not connected to anything, then there will be little effect.  There may be slightly increase current draw as the pin switches on/off, or you enable/disable the internal pullup resistor, but that's all.

If the pin exists and is connected to something on the board - maybe a button or LED, then you will basically be providing an output to that item.  If it's an LED it will flash.  However, if it's a button, and you provide an output opposite of its active state (i.e., provide a HIGH when it normally connects to ground when you press it) and that button lacks any current limiting resistance, then you could risk burning out that IO pin if the button gets pressed.

If the pin just goes straight to a header, then as long as nothing gets connected to that header then there will be no effect other than as detailed in the "pin present on the chip but not connected".