I am beginning to love this thread more and more, because I am actually learning quite a bit of pop-science sci-fi pseudoknowledge, which I absolutely love to death.
Now, because I obviously lack the knowledge of both physics and weapon technology of others in this thread, let me say this as sort of a "dumb question":
In my imagination the best way to use antimatter bombs would be a shaped charge, which something like a 60/40 antimatter/matter ratio. In my sci-fi imagination it would work thusly: Concentrate the gamma burst as much as possible, and weakening the structure of the hull at the same point, by concentrating a stream of energized antimatter into the hull.
Now comes the part where I really am unsure if this would work as I think: In the highly energized surroundings I would expect the antimatter overflow to annihilate parts of the armor - of course on a nuclear level. That would mean that the elements of the alloy change, probably also become unstable isotopes, and themselves cause alpha and beta decay, which then could also further affect it's surroundings.
(Of course, one would assume in the immediate area, everything would break down no matter what, with the mere amount of energy released, so it actually may be completely pointless to begin with, now that I think about it)
If they would really use some sort of sci-fi super-dense elements from the island of stability like Ununquadium, I could imagine it breaking down completely in an array of decays down to a sub-Uranium level eventually.
Also, due to part of the reaction taking place inside the hull, the resulting energy should also be absorbed more efficiently by the hull, while even a shaped charge would waste most of it's energy into space.
As I said, I am really not that knowledgeable about it, and even though we can't really talk about realism anyway, all of the above is just a pile of half thought ideas... I love making things up with the little bit of trivia in my head. I actually had an idea of even more ludicrous ways, involving using sci-fi-plot-energy-fields to condense it into a cascade of small antimatter black holes, which would then burst into a mixture of Hawking radiation and "piled up" gamma radiation as soon as they lose their mass inside the hull. I highly doubt it would even begin to work, but it just sounds so wonderfully, ludicrously absurd.
Now, meson bombs... They are completely up to our imagination in how they are supposed to work I guess? I mean, did they explain it in Freespace lore or did they do what any sensible Sci Fi writer does: Add the word bomb to a cool sounding particle?