In my case I am looking for how much mass flow that will pass. Then I think that the important thing is to see what happens upstream the critical throat.
Yes- You can neglect the friction forces to observe mass flow. I reckon it is a very first step of numerical modeling to keep the model simple. You can then include the friction force to see it's effect on the mass flow upstream and downstream.
In my case I'm actually looking for the effect of the curvature on the mass flow over the mesh clearance in a screw compressor. There it is also necessary to look at the effect of the moving walls. I suspect that only the upstream of the critical section effects the flow through the critical section.