The stock setup is a draw through MAF, but people have run it both draw through and blow through. A car with a mass airflow sensor doesn't measure boost, in a sense, it measures the speed/density of the air passing through it. There is no boost sensor required on a z31, altho it does have one for both the turbocharged cars and the n/a cars with a digital dash.
My input on supercharging a vg30e is to take a pass on it. The amount of work involved is definitely not proportional to the result of it. For the cost of a custom installation (depending on your resources and skill set) would be about the same as a stock turbo swap, depending on price of the supercharger. A stock turbo setup on an n/a engine is good for about 190-200ishwhp with an intake and 3" exhaust on it.
The stock ecu will work, it doesn't care how the engine is receiving air, it just cares how much of it (basically.) You will want to match a turbo ecu up to turbo injectors of the proper year, see the link below for more in depth stuff. You will also need to worry about your o2 sensor depending on which ecu you choose to go with.
The actual engine that the ecu is used for doesn't make a whole lot of difference, just as long as all of the sensors and fuel delivery stuff that are on the engine are correct for that ecu.
linky: http://redz31.net/pages/fuel.html