Sublight missiles are expensive, even more so with antimatter. Loading conventional warheads on them would be wasteful. And, antimatter probably wouldn't do as much damage against energy shields- much more damage to armor or the like. An ion cannon would be suitable for stripping a ship of its shields, while an antimatter missile would be much more likely to destroy a ship.

I take inspiration from the books I read. In the books I've read, there are usually fleets under 1000 ships because of the simple fact that they are much easier to destroy than to mass produce them. With Draconian ships, shields are everything- if the shields fall, the ships are dead.

And note that you can have a powerful weapon and not spam them. Everything has their good and bads- sublight missiles are direct line-of-sight weapons, moving too fast for anything but minor course changes. They aren't warping or anything- they're moving at sublight. Draconian ships use a larger sublight engine to move their ships, instead of engines or anything, with the exception of the transports. Shoot a certain set of vents with a weaker laser, and you could prevent a ship from entering hyperspace and escaping. Hit a different set, and it won't be able to move. A third set would destroy the gyroscopes- the ship wouldn't be able to change which direction its facing. And if a ship can only fire antimatter sublight missiles in a directly straight line, and they CAN still be shot down, even if there has to be some distance, then moving out of the way is an easy way to keep from being damaged. 

In other words:
Sublight = under FTL. A ship at 20% sublight is going .2c
Sublight is like a less powerful FTL drive, with less demand for energy and space
Sublight missiles are too fast to change course- meaning that they are purely directional weaponry, at least on Draconian ships
Sublight missiles are really expensive and act as a currency similar to that in Metro 2033, except more dangerous when used and less common, and not the primary currency.