A lot of times when you make one of something, there's stuff you would make tooling for if you were going to do more than one, but which instead you do by hand. Sometimes this is even true in software, but not very often, because the advantages of being able to recompile something from source code are so huge.
This is true for things like motor mounts and pipe flanges, but not for things like optical surfaces and lathe ways. Even in cases where it is true, if you didn't make the duplicate alongside the original, you have to do the setup again to make a duplicate.
I think your mindset is stuck in thinking about this as an airplane production environment because that was your experience. And your points make sense in that type of environment. But research aerospace in which JWST operates is a very different scale, operating much more at the margins where the tech is less well understood and takes much longer to develop. Investing billions for redundancy on an unproven system is a big risk (besides the fact that it would likely be designed differently - and better - if started today).
The sunk cost fallacy already drives a lot of these projects...imagine how much worse it would be (and how many other, competing projects wouldn't get funded) if the costs were higher.
