So the whole point of culture is to make the planet revolt so everyone on the surface dies? so the DE is counter acted by capital ships and media hubs, so that it's very easily shut down, where as the nova instantly kills the planets population and stops it from being re populated and has a very heavy debuff for a long while after it's been hit. Am I missing something here?
As of the latest Rebellion patch, the balance between the super weapons is actually the best its ever been.
Novalith Cannon - Heavy damage to planet population and health. Planets can become immune to being destroyed however if you have the starbase upgrade that prevents loss to bombardment. Also, the TEC shield generator reduces the population lost, though it needs to be fully upgraded to be really effective. Of course both of these counters are pretty expensive. Its arguably the best though, thanks to the additional half hour trade and max pop debuff which you can't avoid, and thus means the AI uses this superweapon better than the other two.
Deliverance Engine - Used to suck, but its upgrade in the latest patch isn't terrible. Economically, it spreads culture, so you can hurt the economy of a lot of worlds if your opponent doesn't have good culture capacity. It also means the Advent get all of their military culture benefits (shield mitigation, phase missile block, damage for AL). It also applied a stacking penalty to planet allegiance, which makes cultural over throws easier. Indeed, I believe 3 blasts to planets far away from an enemy homeworld causes a guaranteed Rebellion, and there is nothing you can do about it. Militarily, there is also a +25% damage bonus for all your ships in the gravity well it hits, so it can directly affect the outcome of a major battle in a while the other weapons can't. Really the only problem is that this is in the civic tree and you need to get all the culture techs to unlock it. AI can really only use it for its allegiance affects. It's not smart enough to use it on battle fields except by dumb luck.
Kosura cannon - As mentioned, in a skilled players hands its probably the best super weapon by letting you jump all over the map. The damage to structures is minor though in enough shots it can take them out. The disable is more important since 4 minutes (or more with multiple shots) without repair bays can make it a lot harder for a defending player. The AI is the most useless with this weapon though as I've never seen it follow up a Kosura shot with a fleet, so it basically just randomly disables your structures for a bit.