Sure they can annihilate planets, the WH40K battleships have plenty of planet killing weapons. The eldari shoot literal black holes, and these battleships shrug them off like they are nothing. It's easier to just shoot a vortex torpedo at one of these things and force it into the warp, than actually destroying one. I don't think the Federation, Romulans, Dominion, or even Species 8472 has galaxy killing weapons, and that seems to be the level of destruction needed to take down one of the absolute fortresses that are the emperor class battleships

That supernova bomb may cripple the ship, but I don't think it would destroy it. These things have photon torpedo explosions going off under regular operations, somewhat frequently. Sure a few hundred of the crew die, but it doesn't even affect the normal operations of the ship.