If I remember right, it was stated in the command briefing that everyone knows that subspace drives don't work in subspace. Don't remember if it was that mission from when you already got the artifacts from Altair or when you get the new subspace drives and start chasing the Lucifer. Anyway, what saved the GTA and PVN was the subspace tracking info. And fighters and bombers taking down the Lucifer was more like luck, since it was the Bastion that was supposed to attack it.
By the way, I wonder, if you launch a fighter without a subspace drive from a destroyer while in subspace, what would happen in-universe?...