You may run into thermal issues if you leave a bunch of BGA balls unconnected. The chip designers typically assume that the PCB is going to be sinking most of the heat load.
I would have thought that if you are going to attach *any* BGA balls then it is far easier to attach them all, than to leave some unconnected. Unconnected pads on the PCB won't make any difference to the PCB price. While I haven't ever hand-soldered BGAs, having all pads is supposed to make it easier, rather than harder. For example, by pulling the part into proper alignment uniformly as the solder melts and wets the pads.