Is money worth chancing extermination on an assumption that the Shivans can't and won't be able to navigate the fresh, nebular environment? What value would be had for keeping it open, anyway?
Well, these are all assumptions in that sense. You could also argue that sealing off the systems won't contain the Shivans since they made intersystem jumps without using nodes in FS1. Actually, Petrarch even says "we must accept this strategy as nothing more than a temporary measure."
I think there may be something to what Pnakotus said about the nebula density though; it could be that after the shockwave it was possible to move ships through the nebula without any problems.
The Shivans just blew up a star. If ever there was a point at which people are going to be paranoid about Shivan capablities, that point is now.
Also, the Neried was packed full of Meson Bombs, primed, and ready to go. There is no savings in holding it back; there are additional costs (unless you want to just leave it lying around) in safing and disassembly. Deployment cost nothing that had not already been spent.
That shouldn't really matter. As I said earlier, I doubt the security council or whoever will close the node just because they're scared, if there is no (utilitarian) reason to do it otherwise.
As for prepping the Nereid being a sunk cost, that makes a lot more sense. I guess it depends on what other uses there are for the bombs and just how expensive they are to manufacture.
Anyway, I think you guys have suggested a few solid reasons why they might have done this, which is good because I needed that information for a mission I'm doing.