The Kostura shot does not freeze your own fleet, Deceiver. I use the things to support my battles frequently, and I assure you - it's just the enemy that's affected. If it did freeze your own fleet, it would be 95% useless.

Also, if the thing emits some sort of energy, perhaps the Vasari simply polarize their shields to the right frequency (or chain thereof if the energy has an oscillating pattern) to block it. We know this sort of tech exists because the TEC have prototype shields on their Kol battleships that can block a phased missile from penetrating their shields.

I'm not rewriting Britannica, just giving out basic guidelines on the subject. The construction of a nuke is quite simple if you have the materials and machines capable of manufacturing with extreme precision. 
It is a fact that H-bombs can yield 2,5 MT, but they can yield 100 MT and more. The russian Tsar bomb was meant to yield 100MT, but luckily someone under the red flag figured that such big fireworks are a bad idea to set off, particularly over one's own territory. So they decided to go with 50MT.

The point of all that I write is - this game is nothing like the real world, because HERE a single bomber can evaporate a country, while a single bomber in soase cannot do diddly.

Besides, I wrote it mostly because I was bored ;p.

That is true.  Fighters/Bombers currently have the capacity to level a city and in some cases to turn a few city blocks to glass.  It is ironic that these things do nothing in Sins, but it could just be the massive defensive capabilities of shields.  I mean, in the game, solar flares don't exist.  Anything we have today would be destroyed by a big flare, so these ships must have shields that aren't going to budge for much.  

Think Independence Day.  The shields the aliens have completely ignore the nukes we throw at them.  These shields are used to weapons that could end life on a planet, not dinky little nukes...    Even after the shields come down, the nukes still do very little damage to the hulls.  Only when we nuke their weak point (the cannon) does it go boom.  The same would apply to the ships in sins.  These things are far more vulnerable to internal attacks than outward ones (hence the boarding parties in my mod).  

In theory, an Evacuator would be able to take far more punishment than a planet could and remain hospitable.  Planets can have devastating shifts in weather while ships are always at 72 degrees.  It really does make sense in the end that planets by default only have 1500/3000 health and a max of 6000.  Sure, burrowing into the ground is defensive and all, but no one wants to live down there given a choice.  An unsuspecting planet would really have about 100 damage before becoming inhospitable.  Its just that the emergency facilities are exactly that.  They allow the populace to survive despite devastating bombardment.  After all, when a nuke from a Marza hits home, the blast has to be at least a thousand kilometers tall.  That is a REALLY big boom.  That by itself would end life on a continent, a few more would spell doom for that planet's inhabitants.

Perhaps it was patched a some point, but I recall the last time I fired a Kostura on my own fleet, all my ships were disabled, but took no damage.

it did, in fact use to affect your own ships...but its likely they changed it in entrenchment

Error. Watch the movie again.
Nobody in that movie ever nuked a ship with its shields down.
And when they did, the 500-kilometer long mothership turned into a new nebula.

Besides, this is just a movie. Do you think that any of those alien ships could actually DIVE into the Sun's chromosphere and survive? I think not. Now mind that a 10 MT H-bomb, that can be carried by a single bomber, creates an environment about as severe as it is halfway to the Sun's core in a few hundred meter radius.