Yes, well it was in a science fiction story and so why would physics be involved? If you are familiar with Vance's work it has FTL travel and all sorts of other tropes that, well, sound rather Traveller-esque in some ways and RL physics are not invited.
Because ... it's
science fiction? I've got no problem accepting certain necessary tropes to keep the plot moving forward, but:
1. I don't think near-C sand falls into that category - at least not for a setting that plays more like Firefly than like Star Wars;
2. there's all these nice helpful people here who can maybe answer questions like that, so why not rely on them;
3. it'd get awful quiet around here if we didn't ask such questions;
4. it's an entertaining thought exercise; and
5. when I want to play science fantasy, I play Gamma World; when I want to play sci-fi, I play Traveller.
There's no rule against doing science fantasy in Traveller; it's just not my thing.
Aramis' explanation is thought-provoking from the standpoint of our Traveller ships encountering hypervelocity space dust or some such. I'm not sure how much it speaks to the near-C grain's situation. Viewing it on the atomic level, the grain's a dense collection of near-C atoms encountering a dense collection of atoms at rest - at least from the viewpoint of the near-C atoms. "Dense" is a relative term where atoms are concerned - there's more space there than atoms. The grain becomes plasma on the power of uncounted numbers of these tiny atoms bumping into the "at rest" atoms and: 1) being slowed and deflected, 2) accelerating the atom they bumped into (and possibly breaking said atom as well as themselves, I think), and 3) releasing a lot of energy in a manner akin to a particle accelerator impact. Much of that energy is in x-ray, no?
An aspect of the near-C grain's situation is that, unless the impact turns most of that kinetic energy into radiation, the near-C grain - or the superheated bit of plasma formerly known as near-C grain - traverses the distance between outer hull and inner hull that Aramis was talking about, indeed potentially traverses the entire width of the ship, in millionths of a second. Is there opportunity for the near-C bit of plasma to expand significantly in millionths of a second, or will it simply vaporize and accelerate a tiny column before it as it moves along?
Someone pointed out an interesting aspect of the C-grain interaction, that little grain is experiencing relativistic effects: the individual atoms are many times more massive than the "resting" atoms they encounter, therefore more likely to continue on their way with only a slight deviation in course, like a baseball striking a golfball in flight.
What I'm seeing, I think, is a narrow cone being drilled through the ship along with a blast of X-rays and possibly other radiation radiating out from the drill-path. The question then is the balance point - is most of that energy blasting out as X-rays, or is most of that energy exiting out the other side of the ship?
o:
Traveller didn't pass it up 
