I agree that I don't like the black box mentality. I've been using Woodworks software recently to calculate my shearwalls since I can't match it in performance or the shear number of scenarios it analyzes, at least not in a reasonable amount of time. However, if there is a bug in the software I am at its mercy, it just makes me uneasy to trust it so completely or any software for that matter.
Case in point, on a recent job I setup a residential model in Woodworks and the roof lines of two blocks was slightly overlapping. I had a hunch that the software would not like this area of the model however I was trying to create as realistic a model as possible. When I looked at the loads they seemed a bit high to me, so I then compared the diaphragm and shear loads to a similar structure with all of the same design criteria within the software. Sure enough the loads were about 40% higher. I removed the offending geometry from the model and it then brought the loads into the expected range. My feel for what the loads should generally be was vital to getting the right answer in this particular case. Had I blindly followed the software I would have significantly over designed the shearwalls.
For wind loads calcs I think it is important to at least go through the full procedure a few times to understand how the numbers are arrived at, however on a practical level the calculations should be either tabulated or programmed into a spreadsheet and then manually checked to verify their accuracy. With my calculators I have checked them against different sample problems found in ASCE publications as well as more recently against the Woodworks software. Even so I cannot guarantee they are without error or my method for computing overhang forces (envelope procedure) may differ slightly from other software.
A confused student is a good student.