3kt? that's physically impossible, plus we don't know what kind of explosive it is toting
Well, it could be 3kt TNT equivalent with a Plotdeviceonium warhead for all we know...
Furthermore, a true 5000mt explosion would have ripped the Lucifer to shreds. It may be the size of a large city, but a city can be easily crushed by a Davy Crockett Rocket, so imagine what a true 5000mt explosion would truly be capable of. I know it's more devastating in an atmosphere, but it still would have sploded everything.
Nukes aren't that powerful in space. A lot of the devastation of a nuke comes from it's shockwave, which needs air to be carried. I guess with all the sounds and the way shockwaves are moving through space, one could argue FS has "space air", but I think we are still to believe that there is no air in space.
Still, a 5000mt explosion should probably shred a lucy, and about anything else. The fact that it doesn't seems to mean, that materials are used that are so much more sturdy that anything we have imagined so far. As the GTVA and UEF vessels can take that sort of punishment as well, I guess mankind and Vasudankind have developed something to that effect as well. Who knows if thermite would even do anything here, it burns really hot, but perhaps the material is indeed able to withstand temperatures like within a star. Maybe it isn't even metal, but some sort of plotdeviceonium-gameplayproofingum quantum crystal thingymajjiger alloy. Or perhaps electromatter... no, wait... the ships aren't pink...
I guess it could be used, however, as a sort of genocidal weapon. Dumped in sufficient numbers it would overheat the interior even if the hull could not be significantly compromised. That could kill the inhabitants, leaving the ship for the taking. The amount of thermite that would have to be used would be rather impractical, though. I could imagine that you'd need huge, thermite laden carrier ships to deploy it, which in turn would be a vulnerable and fragile target, easily baked and obliterated.
Speaking of "I thought of a weapon no one else did"... When you have AWACS in the combat zone, and you are able to coordinate such extremely precise jumps to allow SSM strikes, why not jump in a harbinger INSIDE the ship. 5000mt inside a ship would destroy the interior, or at least kill everyone inside, even with a plotonium-whatever alloy as a hull. Ah, I guess every ship has some sort of shielding against that, probably the "Gameplay > Everything" device, which is not targetable as a subsystem.
I still support the UEF a lot more than the GTVA.
And to make myself completely unlikeable: I think the Gefs have a sensible idea, which should be put into action if complete xenocide of our species seems absolutely unavoidable.