In FreeSpace, I have to say that the values given in the tech room entries of some missiles in the units of kilotons and gigatons, are wrong, depending on which source you consult and what you consider canon.
In FreeSpace 2, we see a Hercules fighter that hits a planet in Deneb, leaving a small line of debris and a trail where it hit the ground. Something with that much mass (capable of withstand nuclear impacts) would probably exert enough force moving at that speed to make a jolly big crater, even if it's not that large. However, it is possible the pilot was able to maneuver his Hercules to a speed slow enough to land, but lost control at the last moment and crashed. So that's up to discussion.
In a "super secret" cutscene in Silent Threat, however, we see a Thoth fighter flying around. Then a Shivan "space marine" jumps out of nowhere and lands on the fighter, shaking it up, before smashing through the cockpit with a claw. Tell me, is it possible that a ship that can withstand nuclear impacts can be taken down by a nekkid Shivan punching the cockpit? I doubt it... Either the cockpit is extremely vulnerable, or that cutscene was non-canon (though it was released by Volition it may have been a test cutscene of some sort).
A possible explanation for this inconsistency is that the kiloton and megaton units have changed since the 21st century, and are no more kiloton and megaton of TNT, but a kiloton or megaton of some other weaker explosive that isn't so dangerous (which is a sort of stupid thing to do, IMO).