Missing pads allowed on BGA?
Yes and no. You can omit pads if you wish however, the following issues can occur.


If you run traces under the ball and trust the solder resist to act as an insulator you are likely to get shorts or insulation breakdown/capacitive coupling through the resist. It simply is not intended for that purpose.
If you remove too many pads you are reducing the mechanical stability of the device attachment.
If you remove too many pads you will be reducing the thermal conductivity of the device to the PCB and may incur greater heating problems with the device.


As such, it is recommended that missing pads be kept to a minimum and no traces should be routed under the pins.

EDIT: If the pin on the device is an unused input and there is no issue if there is a short to the underlying trace, fan-out etc, you could get away with it... but really, if that is the case, then just wire it that way and keep the pad in.