Heat is a much larger problem in a vacuum then in an atmosphere. In a vacuum cooling is accomplished only by radiation and that is basically at very low rate unless the object is quite hot. Cooling is the biggest issue that a warship would have, as waste heat would build up very quickly. Attack Vector Tactical or Mass Effect are essentially correct on this point; the former messing up how their heat sinks would work since they violate the thermodynamical law that heat flows from hot to cold (the heat sink can't be hotter than the object you are sinking heat out of).
If you have a mass driver launch mechanism then you do not have a "box" launcher. You could use a cold launch mechanism (gas blast) but that would slow down your launch rate again since no matter what you do, you would not want a collision between launching missiles...you would get also a staggered powerup to ensure that again a failure doesn't happen and so on. There is no reason you can not say that a box launcher fires but a single missile per 5 s (or whatever) interval. That would still leave them useful for larger missiles and for convience but not make them so overpowered that they are the only sensible option.
Small missiles are nerfed the second that you stop using ablative armour, until you do that you are bandaging a sucking chest wound as far as I am concerned.
There is nothing wrong with a limit on how many missiles a ship can command per fire control but the reality is that becomes irrelevant as the mass of a fire control is not significant and so if I have 10 of them rather than 1 it won't alter the situation that much.
I'm certainly not going to argue whether Box launchers can use a rail-gun mechanism or not. I don't know how much space it would take with technology that exist in Aurora.
I know that heat is a bigger problem in space, so I didn't mean that the heat in and of itself was the problem, rather that it's easier to propel the missile out from the ship without igniting the missile engine due to that there is no gravity pulling it down.
Although, the gauss principle would probably be more probable and should take very little space to propel a missile a few dozen meters in a matter of seconds.
The thing about fire-control is not so much the size as the cost, fire-controls is very expensive.
I do agree with the ablative armour style mechanic. I do like the Newtonian aurora damage model where the armour model is better and if we had that I would be quite happy. Here, armour will have some minimal resistance and can withstand smaller damage without being destroyed. Nuclear missiles would not intercept ships either which is quite ridiculous given their speed in Aurora anyway.
With 6.3 we will get chock damage which obviously will make a missile with larger warheads much more important. So there will be some band-aid mechanics in place to spice things up.