Finally something I know a little about...
NASA uses MIL-Spec fasteners, for quality reasons, on hardware that it designs. I'm guessing that some NASA organizations use metric fasteners, but in the US, metric MIL-Spec fasteners are often long lead and EXPENSIVE. As an example, we had the option of a #2 or 2mm flat head to fasten a small gearmotor to a mechanism. The #2 was like $1.90 and in stock. The 2mm was $25.00 ea and 10 weeks lead time. Not kidding.
One of the comments on Toolguyd mentioned standardizing the sizes. If you did that, the lowest common denominator might be something like 3/8 or something that just would not work for smaller applications. America bought Space Station modules from several different countries, Italy comes to mind as one. NASA did not put requirements on them as far as fasteners go, so they probably used metric. Also, payloads have many different countries of origin, so fasteners could be most any shape, size or standard. Yet another factor is that NASA has tried to lower costs by using as many off the shelf components as possible, and again, no chance of fastener standardization for those.
The boxes shown on Tool Guyd are for internal use. For EVA, there is some standardization. Anything needing to be actuated during a space walk is required to be 7/16 hex. Not sure why that particular size became the standard though. The shape is detailed in the EVA equipment standard. There can be exceptions, but they require approval. Now that I think about it, there may be other sizes, but the preference is to use the 7/16 hex. As you might expect, the EVA toolboxes are somewhat less extensive than the IVA boxes shown.
That's all I know.
But since this is my first post, I would like to thank all of those who have contributed to the journal. I have learned so much from this forum....
Glad I could finally contribute.
Scott