Who knows why? Maybe they blew it up at the end of the trip because they wanted to give escaping ships more time or because they wanted to make sure nothing can get in from the other side.
That makes no sense. The collapse of a node has only (as far as we know) happened twice before that point, and both times weren't exactly ideal situations to run experiments. So the GTVA has little basis to reasonably guess how long it would take the node to close after detonation. And the more time that the Nereid was in the node, the more time for the Shivans to send fighters and blow it up, or for something to get in the node before it collapses.
I'm guessing that they wanted the ship as far from Vega as possible. It's also possible that a ship needs to be partly in and out of subspace to close a node; both the Lucifer and the Bastion were seen as being half-in half-out when the big boom occurred. Or the GTVA may not actually know whether a ship has to be part-in part-out of the node and just did that to be on the safe side.
