Not 100-megaton antimatter's worth, no, just missiles that have up to 100-megaton's worth of explosive power.
Antimatter is a powerful weapon. Of course, it wasn't exactly meant to be detonated all at once while inside a ship.
The good thing is that even if you get a temporary breach of their shields, and pass your lasers along as much hull as possible, the chances of NOT hitting a high explosive before the shields block you out again is very low. In tight formations, a single Draconian transport being destroyed or self-destructed would probably have a temporary EMP effect on the nearest ships, and scramble sensors and the like for any ships within a medium range (relative).
And transports are slow- if they manage to ram you, that's like getting killed by a Medic bot in Robocraft.