Custom-making vertical downpour showerhead from copper pipe?
What you're going for is flow and velocity to make for a good feeling shower.  There is absolutely no reason to assume that the cross-sectional area of the nozzle has to match that of the pipe, in fact you don't really want it to, you want the velocity coming out of the nozzle to be higher than that in the pipe, that's why you have a nozzle.  At any rate, the pressure drop across 256 (shouldn't it be 64?) 1/16" holes is a lot different than that across one 1/2" hole.  

Nozzle making is tricky because there's a lot more that goes in to it than just the pressure and velocity.  There's friction, edge effects, and contraction at the holes.  There's even, as gbronner says, pressure drop through the line, but in a 3/4" manifold, the drop should be very small.  I'd say your best bet is to experiment.  Start with a small number of holes and work your way up until it feels right.  Looking at my own shower head, it has 45 holes which all look a bit smaller than 1/16th inch.  So maybe I'd start with 30?  The fewer

Your biggest problem will be getting them to point where you want them to go.  That can be a bear and I'm not sure I know of any way to solve that other than to drill and deburr the holes very carefully and, again, experiment.  Maybe even just start with a few.  You may be surprised at where the water wants to go.