
To me it actually seems the Vodyani faction quest's branching path is designed that way: Religious path asks you to capture enemy home systems, while the Heretic path asks you to build a planet destroying ship (though it doesn't directly ask you to destroy home systems).

The Cult in EL had a similar ability since they were the only faction capable of razing enemy capitals. Like you said Planet Cracker is usually unlocked way too late and is too expensive to produce and takes too long to charge to be of any practical use, but I think one possible late-game use would be destroying capital systems, thus reducing the number of capital systems required for Supremacy victory. Now while that makes sense for such a destructive weapon just for it to destroy planets with little yield to it is kinda wasted time when you could've researched better things and spent time making other ships to outdo the enemy. It doesn't help that the tech for it is at the very end, it can take a great deal to make a ship with the module and it takes several turns to charge it up for just one planet A system of 5 planets takes 25 turns to destroy, that's a lot that could go on during those turns. So it's mostly just useful in very very few cases when you're ahead, managed to get ahead or the enemy is distracted by more than one enemy.

That said, if the enemy is even close to your power level or above, it's practically impossible to make use of it cause the enemy will have fleets to disrupt you and building that ship and tech will have set you behind in terms of power. Though personally I think they should add a way (except privateering) to take over systems without colonizing them, which would make this tactic even more flawed, even if you have to make sure the enemy don't recolonize it. Only reason I can find other than just giving your enemy the middle finger is that allows you to "take over" a system without capturing it and destroying everything they built in one go.

It should be a win-lose situation on a galactic scale, as destroying a planet shouldn't be a small thing, but it also needs its bonuses too given how hard its to achieve it. Such as destroying planets in a whole system can destroy the hyperlanes or allow you to gain a limited amount of resources from those planets (I believe Stellaris is doing that for their planet crackers), while also giving diplomatic and approval penalties. Personally I'd want more mechanics to it, both negative and positive.
