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.