Through a friend-of-a-friend, I did actually manage to get a copy of the source code to CTSS, the cray time sharing system, on microfiche from Lawrence Livermore National Lab, and I even had it digitized (but not OCR'd), but it's written in a language called COMPASS i've never found a compiler for.
From what I've heard, part of it relates to volume. If someone asks to declassify a single page document, it is pretty easy to evaluate it and decide whether it can be released or not. Presented with thousands of pages of old source code, it is an immense undertaking. Added to that, people don't understand the old source code any more, and worry that there might be something lurking hidden in there that should not be released, but they might not notice it due to not understanding it.
I hope at least they never destroy any of this old stuff, and maybe one day (even if only decades or centuries from now) the US government will decide that enough time has gone past that it no longer could pose any risk.