It doesn't make any sense in either era. You have to accept some amount of gameplay-story segregation.
Possibly, however, remember that there was a subspace missile strike weapon made for FS2, although it didn't make it into the canon campaign. Warping a supply of inactive missiles into a ship isn't too dissimilar, although keeping the subspace node contained inside a ship would be... problematic, to say the least.
By War in Heaven (yeah yeah I know it's not canon) the Tevs might have been able to do it, seeing as, by then, precision subspace jumps and SSM strikes were commonplace.
Regardless, it's highly probable that this is how the Ancients did it. Remember, in their prime, they were about the same level of FS1 GTA/PVN in terms of armor and weaponry, but far more advanced than post-Capella GTVA in terms of subspace.