You know what, I figured it out. The shields aren't to protect the Sa-Matra from the fleet, they're to protect the fleet from the Sa-Matra!
The Sa-Matra does not only have weapons of tremendous power, it also has weapons of great subtlety. Unless encased in this shell, whoever is at the helm could invisibly turn the tide of the battle.
Or at least, the Kohr-Ah think so. So into the shield it goes, and the shield generators go on the outside.
How does that sound?
That does make sense. That would also be the reason why the Sa-Matra does not use its primary weapons to defend itself and instead lauches those 'drones' to attack.