First of all, very nice! One note on the "fusion cooling system".
The big problem here, is that your turrets won't heat up beyond 1000 kelvin, maybe. The melt down if they get hotter. That also means that you can not heat up your coolant beyond 1000 kelvin. Therefor storing energy by fusing atoms together is impossible, because you'd need a lot of energy to create that gradient. Again, more energy is needed as investment than you could dissipate and that's why this idea won't stand against physics.
In space however, energy dissipation of a "shockwave type" (i.e. kinetic) could only apply to the few actual components of the bomb (casing, core etc.). That means that in space, most energy of a nuclear explosion is just radiated away (also because there is nothing which could absorb the radiation), while only a small amount of it results in a (probably very high) acceleration of the bomb's fragments.
The same applies for a (hypothetical) TNT detonation in space, but as the radiation of such an explosion is of much less energy, the relative fraction of kinetic energy "blown away" should be much higher there.
Well, don't forget the expanding gas of your warhead. All your TNT turns to gas during it's reaction phase and that gas usually expands at sound-speed if it's in a vacuum. (Note: Sound speed for this one specific gas, it can be far more or even less than just 330m/s) So you'd still have an kinetic effect with a hot particle wave hitting your hull.
Rather a "bug" than a feature. But think about this: Warheads in FreeSpace only damage a spaceship properly if they directly hit the hull. If you shoot them just meters away from the hull the damage by the shockwave is trivial. Suits the explanation but as far as it goes for things like "16.5Kt per MX-50". Just ignore those numbers, they are bogus and no one at Volition actually did the math on those. They're supposed to sound cool. Let's take the Tsunami bomb, for example:
Intelligent tracking similar to GTA targeting system - prior to launch, communicates with ship computer, gathering data about enemy target types and whereabouts - slow, low maneuverability - antimatter warhead (500 tonne3 mass-to-energy conversion) - due to instability of antimatter, no more than 10 may be carried on board a GTA bomber at any given time, unless pilot is granted a special permit by an appropriate governing body.
500t mass to energy. First of all, it is pretty clear that this bomb does not weigh 500 tonnes! But it would have to for this yield. Antimatter and matter explosions convert their full mass to energy in form of radiation. Electromagnetic radiation. Let's do the math, here:
1kg ~ 89875517873681764 Joule
or 89.876 Peta Joule
Why?
E=mc^2
E = 1kg * 299792458 m/s * 299792458 m/s
E = 1kg * 89875517873681764 (m/s)^2
E = 89875517873681764 Joule
As conversion:
1kt of TNT = 4168000000 Joule
or 4.168 Tera Joule
That is, one
kiloton worth of energy is released in the conversion of 0.04658 grams (46.58 mg) of mass.
Little Boy yielded a 13 kt of TNT equivalent.
The amount of energy if just 1kg of mass is transformed into energy is incredible and can be compared to 1.6 million Hiroshima bombs (Little Boy). Keep in mind that antimatter warheads don't create a shockwave as we know it but an expanding sphere of dense radiation (heat, gamma radiation and so on) which travels at light speed and would kill any crew member on the battlefield practically instantly. There is no known material which can absorb these amounts of energy and radiation. If it does, it would melt down as well, instantly turning into plasma. (And this comes from only 1kg). The Tsunami yields 500 tonnes. Do the math, yourself! Not even "special armor materials" would withstand that. Nothing in our universe does. A real planet cracker!
These bombs would incinerate the whole battlefield in one blow just with their radiation output. It's pure fiction, not true and not even reasonable canon because even though this flavor text exists, it's not present like that in the game itself.
There is atmospheric combat in Act 4, and I can guarantee that the ordnance thrown around doesn't have a payload anywhere near 16.5KT. Whenever FS (especially FS1) tries to throw around numbers, they're nonsensical, and we're ignoring them completely.
Which is a good thing to do. Hit an F15 or B2 bomber with a Hiroshima Bomb at point blank range (10m) and ignore the shockwave in your calculations. Just take the heat from that explosion. You'd still end with a puddle of molten metal. I'm sure a GTF Hercules wouldn't react differently if the MX-50 really had 16kt. ^^