Overconfidence, perhaps, or lack of need? The Lucifer cut through everything in it's path just fine.
I also wonder if they can't practically be launched/stored from fighterbays and loading machinery meant for normal-size fighters. AFAIK, they always appear from subspace, and never from a fighterbay(we've seen Nephilim launch from a destroyer, but not Seraphim). I imagine this isn't a problem for Sathanas bays, though.
Maybe they actually have to unpack, assemble, and keep them at the above fighter repair centers(or something similar). Given Shivans don't need environmental suits, they could easily get pilots into them without needing an Azrael to individually dock with each bomber.
If Seraphim cannot be launched from destroyers, they might have had trouble keeping up with the Lucifer fleet(as the GTA certainly did), and were thus unable to participate in the main Shivan thrust, and thus only came into play when the Shivans were put on the defensive.
EDIT: That's right; we also know the FS1 Shivans had Nahemas or some other very similar bomber class somewhere, from the existence of the Sekhmet as an HoL design/prototype, yet neither appeared at all in FS1/ST. That's an odd one to have to explain, given the Vasudans never seem to have reported the Nahema to the GTA. It would seem to suggest that the Shivans used the Nahema exclusively in HoL space, or the HoL seized Shivan cargo that happened to include Nahema parts(and the FS1 Shivans still never fielded them at all).