This is a carefully written question that deserves a better response than I can give it. My basic answer is, "I don't know". I can give you some hunches, but you should be aware that they're based on the same kinds of first-principles reasoning that I'm so skeptical about in other people's HN comments. So:
* I have been very unimpressed with the quality of NSA "TAO's" tooling, and, when I have conversations with people closer to NSA offensive cyber stuff than I am, what shakes out generally is that they people at the tip of that particular spear tend to be super young people in basically their first ever software job.
* But Stuxnet was sort of impressive.
* But then, what was impressive about Stuxnet was domain knowledge about a particular piece of industrial equipment, not hardcore computer science. The software engineering details of Stuxnet were kind of unimpressive.
* But there's Flame, which is impressive in a CS kind of way.
* NSA's original advantage in these kinds of systems probably stems largely from the fact that they were a monopsony buyer of cryptographic talent for many decades. You'd expect there to be a period of catching up.
* But cryptography is now one of the better known pipelines for applied mathematics research, particularly for people who cross over between math and CS, and there's a lot of those people, so it's hard to see why NSA's advantage would be sustainable over the long term.
* But also NSA does have a sustainable advantage in the kinds of cryptanalytic work that can only be done with massive, specialized compute resources, and for all I know when you can casually conduct research on gigantic ASIC clusters as easily as I can fire up Sage and add generate a curve point, you learn a whole bunch of stuff that is broadly applicable.
* But academics get to collaborate directly with everyone in their field and NSA not so much, which is a mitigating factor.
I think it's very healthy that we assume that NSA has space-alien capabilities. It adds rigor to our security models. And again I don't think we should use things like SIMON and SPECK.
I just don't think we have to stop talking about the engineering aspects of SIMON and SPECK simply because they came from the NSA.