We have no reason to believe it's possible to open a subspace portal in a solid or even semisolid object, and because it's never done or attempted and our fighter's drives won't let us, every reason to believe it's not. BUT, nebular missions suggest the possiblity of opening one in what amounts to an atmosphere. However given the probably superb compartmentation of GTVA warships and their motion, it would be difficult or impossible to open a portal because of the size of any practical weapon to use against them. Cyclops, Harbingers, even Tsunamis are easily the size of a man, and the subspace portal is usually at least twice the diameter or height of the object it's transporting.
As such, most cruisers and corvettes are simply immune, as there are no spaces aboard large enough in both dimensions for the weapon to arrive in. Destroyers are still possible because of the fighterbay, in theory, but in practice the details of targeting such a thing are simply unlikely, even (and especially) for the Shivans.