I'll chime in to point out it is indeed very possible that the destruction of Capella was "never explained" internally, because it never needed to be. I've always maintained that the Shivans are such excellent opponents because we know almost nothing about them. The "hard data" about them in the Tech Room is itself mostly conjecture, and whenever we learn more about them it only serves to highlight how little we actually know. Ever wondered why every new piece of information about the Shivans gleaned in the FS2 campaign has multiple ambiguous interpretations?
I'm going to bring up the first Space Sim I personally played here: Wing Commander Prophecy. Anyone who's read the booklet that came with the game knows they did a very good job building up this ancient and technologically advanced "boogeyman" of a species as the possible nebulous perpetrators of a system-wide purge, and the first encounter with them in game is at a debris cloud of an entire Kilrathi fleet. The comm chatter you hear from their fighters is initially jibberish, and for a while they might almost be scary.
Until they learn English and start getting their insectoid hind parts handed to them on a platter. For all the "horrible star gods" mythological build up they turn out to be just a new player in town with comparable technology to yours, and a single carrier stops their invasion (assuming you don't then continue the story with Secret Ops anyways).
Volition didn't make that mistake with the Shivans. They gave us a Pyrrhic victory in FS1 and a desperate fighting retreat in FS2. When it looked like the playing field had been leveled they showed us a fleet of Juggernauts, WAY more then would be needed to utterly destroy every system in the GTVA. Only they weren't doing that, so the closing mission doesn't even give you the satisfaction of believing you "stopped" the Shivans in any way, or even hindered them!
The end result is a foe who started terrifying, and ended even more terrifying. Explaining their motivations would only diminish their alien nature, and the horrors the paranoid mind can concoct in a dark room are always going to be worse then the monster that's actually there when you turn the lights on. So I'm not convinced Volition even felt the need to EVER explain why they blew up Capella.