This assumes that the GTVA can target accurately enough to do such a thing, which, by all appearances, they cannot. (The Shivans might, probably even can.) Also, it occurs to me that we aren't even sure you can open a subspace portal inside an object. The Sathanas juggernauts managed to do so inside a star, but apparently with difficulty. A ship would have a much higher density.
We've also seen GTVA ships and NTF ships jump into asteroid fields, apparently without worrying they're going to end up half inside an asteroid, and despite the fact GTVA subspace technology is manifestly not very accurate. I suspect it's simply not possible to open a subspace portal inside something, or even particularly close to it in relative terms; we've never seen a ship ram another out of subspace in anything canonical.