If you have a terminus est, you almost definitely have a fleet to use with it if you care about using it in a game. As such, you have more launch bays.
Why not just model it with 2 launch bays and one hive/battery. Call it 3 on each side (like the styx) and 3 on the prow. I don't really think the problem is with the launch bays, necessarily, but in the batteries, lances, and special rules.