What? I'm not questioning whether the weapons research actually happened. I'm questioning the sincerity of people claiming they didn't know what they were doing. I've seen plenty of weapons programs. They aren't a secret to the people working on them. My point is, the government doesn't need to lie to researchers or even pay them very well to get them to develop weapons because there are plenty of intelligent-enough people willing to do it almost for free.
Lots of people working on the Manhattan project did not know what they were working on. The core group of physicists did, but not many others.
Because working on things that go boom is like working on fireworks. The fact the end up on people is incidental.
If "This doesn't fit into my mental model, so everyone else must be lying" is how you deal with things you didn't personally experience, do what you have to.
I've worked as a contractor for a safety system that turned out to be for a foreign military. I was given a signal, and told to write software to fit it. The signal could plausibly be collected for a wide variety of civilian purposes.
What I realized later was that none of the civilian markets could possibly justify the cost of the project.
The particular type of signal fitting I was doing was only achievable by a few thousand expensive domain experts in the world, so, I think that addresses your other point.