The 'some reason' indicates that he realizes that *something* happened to stop them from firing their last set of weapons - he just doesn't know what. If he belived that the Landreichers had destroyed the cruisers quickly enough then it wouldn't be an issue. Given his previous conversation with Jukaga, he seems the most likely to figure out exactly what happened...
He knows that they didn't get the strontium-90 nukes off, nor a second wave of antimatter missiles, and is very thankful that this was the case. He didn't appear to be brooding on the matter, given that he was busy thinking about how many people had been lost due to the civilian government as well as the high-ranking traitors who rammed through orders which defanged the Confederation Fleet even as it gave time for Thrakath to rearm and rebuild his previously-depleted forces.
And you're right - he's probably the only one who would suspect that someone had stopped the nukes, but at the moment he'd had other things on his mind; the heavy casualties, Kevin's MIA status, the near-total annihilation of several colony worlds, and how Thrakath had seriously underestimated them... and how much it'd cost the Confederation to stop this last incursion. As he noted himself, the Confederation had 'shot its bolt' and now was going to be scraping the barrel in order to pull together the forces needed to successfully prosecute the war. They'd lost their advantage, several shipyards, and a whole lot of crews and carriers in order to halt the advance, and would be in dire straits should Thrakath get the rest of his fleet online (which he did by WC3, a year later).
The situation doesn't seem to have been noted by Thrakhath; his reaction seen just before the end of the book is that at least Jukaga is dead.
Again, neither Tolwyn or Thrakath were thinking too deeply about what had just happened; one was thankful that the nukes didn't go off, while the other was shocked both by his defeat as well as the fact that he'd lost another opportunity to push the war to a successful conclusion, as his father had back during the early days of the war. In both situations, one more carrier would've been the crucial reserve that could have pushed both fleets to victory. Although, to be fair to Prince Gilkarg, Admiral Nargth was as much to blame for the defeat as his father was - if they'd pushed on with most of the battleships to intercept the suicidal run that shot down all those transports, they could've probably taken and held McAuliffe, then finished off the remnants of Task Force 21 and Seventh Fleet.
But at least Thrakath knew the Baron was on that ship, and had been against the nukings. He would've probably been able to come to the same conclusion that Tolwyn may have (eventually) come to, given that he had similar information (if not the private communique between Tolwyn and Jukaga, where the latter basically apologized for what was about to happen to Warsaw).
Also, it's important to note that Jukaga didn't save Earth because he loved humanity - he did it because he realized that the human reaction to such an act would be the quickest way possible to a Kilrathi defeat.
No, he didn't love Terra or humans, but neither did he want to see them wiped out. Remember that he wanted to use them and their resources to stand against the Mantu; that's why he argued for trying to get them to surrender, and why he pleaded with Tolwyn, then the Senate, to surrender and save their worlds. They would be useful, given their numbers and inventiveness, even as they were dangerous because of them.
It's not clear that Jukaga is 'in command.' His assignment is given off screen and all the Emperor orders is that he be given a position of honor. He's definately not literally commanding the cruisers during the final attack... a Kilrathi captain gives the orders for the ships to target and fire their antimatter weapons.
No, Jukaga's not in command - but he was initially put in with the fleet as a representative of the clans, and because the Emperor wanted him disposed of after his failed assassination attempt. He was there to hold the flag, and to make sure someone witnessed the victory in the name of the rest of the clans. But at the same time, he was put in there as an important figure, which given his reluctance to nuke the Terrans, made his position as an observer/etc of their destruction more 'fitting' in the eyes of the Emperor, I suspect.
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