The Kostura has three effects. The first is that it deals a small amount of damage to all enemy units, the second is that it stuns all enemy units for a short time, and thirdly it makes the target planet a phase stabilizer node temporarily... as in it's as if the planet has a friendly phase stabilizer there.
The Kostura damage is inconsequential unless you have 10 or so Kosturas, then it becomes gamebreaking since you can kill massive fleets very quickly (if the target planet is too far away, a smart player will run his fleet out of the system. If it's close enough, though, the first Kostura will hit before he does this and stun him long enough for the others to arrive. Very annoying, essentially a free win for the Vasari if they get this.
You can use its stun capacity in combat. It doesn't affect friendly units, so just fire into battle and then get some free attacks off. If you're really feeling nasty, you can deploy mines immediately after the Kostura hits. The enemy will be stunned while the mines arm, and then they will be destroyed by the minefield you just created in the middle of their fleet.
Powerful as that may seem, the Kostura can do even MORE. You can use it to turn enemy planets into phase stabilizer nodes. This allows you to completely bypass front-line planets and jump directly to any planet you shoot with a Kostura. If you want to directly attack their homeworld, you can do so.
So yeah, the Kostura is the most powerful superweapon by a massive margin. The others just aren't even in the same class.