I support Wes in this, not that he really needs it but...
Maybe I see things a little different from most people, but to me the issue is game balance (if that can be applied here), how would multiple shield setups enhance gameplay? In my opinion it wouldn't, as it would very easily start an arms race and make almost any other vessel without a multi-shield system obsolete.
Imagine if two fleets are facing each other down, one side fires their BBQPWNAGE weapon at the other, and gets laughed off by the OMGWTF shield, "WTS!" cries the first fleet "Our BBQPWNAGE weapon no longer PWNs, we need something bigger!" and the cycle continues.
Also, try to remember that just because a weapon can laydown an uber-pwnage amount of firepower, doesn't mean it will always hit, to my understanding the GM makes most of the calls in ship combat.
Yes, I'm a noob here. I claim no industry or roleplay experience, but I have had numerous discussions about game balance on another project, and I look about fleet combat sort of like a dice game or computer game.