The old super weapon (if that was the nova-bomb, I fail to recall) was all about doing something funky with ship jump drives causing them to overload and detonate while keeping your own drive safe. So less a nuke and more some sort of specialised emp/feedback weapon.
For normal ship to ship I imagine actual nukes would perhaps be less great, you're either close enough that you are going to get yourself fried along with your target or far enough away the other ship can dodge or shoot them down.
Still, versus stations or capital ships it sounds like a reasonable plan. Then we have to hand wave "it's a game" and probably leave it at that. We could perhaps argue something with point defence or something or maybe say shields are for some reason specifically good against nukes but we don't see that long range point defence (still I said this before with small ships so, hmm) and when the shields come down why wouldn't you?
Perhaps there is a treaty against it like with AI's...
But versus Thargoid sites? Seems like an obvious win, like wise dropping asteroids on them - probably harder to stop that!
So, "it's a game" then
