I personally cannot see the point in equipping a mere transporter with the devestating firepower of a Sathanas. It does seem that Shivans are hellbent on domination and extinstion of anyone who dares to cross subspace so my personal theory was the Sathani were deployed as revenge for taking out their planatary destroyer The Lucifer. After all, does it not say on the box of Freespace 2 "They want to know what happened to their scouting party".
Going back to The Ancients monologues, I realise I'm clutching at straws here, but I personally believe that the Sathani are only a somewhat recent developments created 100s, not 1,000s of years ago. In their 2nd monologue, it says "when the destroyers came for us we attacked, never had we been defeated. They were like the others.... only these were not like the others; they did not die". I therefore believe that The Ancients only encountered A if not The Lucifer type destroyer.
I say this as is it not claimed that The Ancients were the same as us techologically, and so therefore may not have developed weapons to counteract shield techology; "We have the knowledge, but not the means. and so this is our legacy. In subspace they cannot use their shields and into subspace they can be tracked".