Wikipedia links to this guide to the APP, published in December 2006 (much closer to when the rule itself came out): https://web.archive.org/web/20191007132037/https://www.bis.d.... At the end of the guide is a list of examples.

Only two of these examples meet the definition of vector processor, and these are very clearly classical vector processor computers, the Cray X1E and the NEC SX-8 (as in, if you're preparing a guide on historical development of vector processing, you're going to be explicitly including these systems or their ancestors as canonical examples of what you mean by a vector super computer!). And the definition is pretty clearly tailored to make sure that SIMD units in existing CPUs wouldn't qualify for the definition of vector processor.

The interesting case to point out is the last example, a "Hypothetical coprocessor-based Server" which hypothetically describes something that is actually extremely similar to the result of GPGPU-based HPC systems: "The host microprocessor is a quad-core (4 processors) chip, and the coprocessor is a specialized chip with 64 floating-point engines operating in parallel, attached to the host microprocessor through a specialized expansion bus (HyperTransport or CSI-like)." This hypothetical system is not a "vector processor," it goes on to explain.

From what I can find, it seems that neither NVidia nor the US government considers the GPUs to count as vector processors and thus give it the 0.3 rather than the 0.9 weight.