How is the flow of air through a NACA submerged inlet determined? This question pertains to the design and/or selection of NACA submerged inlets. I am trying to understand what kind of airflow would enter a NACA submerged inlet/scoop and am looking for a good reference to use.

Suppose you have a typical NACA submerged inlet , which has a 2.75 inch diameter hose connection (so an area of 5.94 inch2), and you are flying at 100MPH. How much air actually enters the duct? 

I've seen the famous NACA 5i20 Report but can't seem to find the answer or don't understand it fully yet. The report routinely compares the inlet air velocity (Vi) to the free stream velocity (Vo), calling it a ratio "Vi/Vo". It then shows pressure losses for various Vi/Vo ratios. But how do you know what Vi your scoop will get?

I've thought about relating the mass flow entering the duct area (the triangular part) to the mass flow through the inlet, but I'm not sure if that is the most accurate method.
The flow through the inlet is determined by the resistance of everything behind the inlet. If the inlet is blocked off internally, there is no flow and $v_i$ = zero.

The mass flow is indeed the way to determine through-flow: mass in = mass out. Which is a function of the pressure build-up (both in and out), cross section area (both in and out), temperatures, etc. A similar process occurs in a jet engine inlet.