This is something that comes up in narrative from time to time, and older games tried to incorporate it, but I don't know the best way to handle it with EotE. Since I've been trying my hand at designing ships lately, and I have a few Mon Cal ships, this is rather relevant to me right now.
Mon Calamari ships are known to have some of the best shields out there, mostly due to having backup generators to ensure that there are always shields. With that in mind, I can only think of the following ideas to incorporate that into the current rules:
1) Increase all shield bonuses.
2) Count it as a "backup shield generator" customization, granting a +1 (or two +1s for Silhouette 5 ships) to a shield facing.
3) Negate a critical hit against a shield system.
4) Reduce difficulties to do any work to shields (repair, angle, etc).
5) A combination of 2 and 3.
Anyone have any thoughts there?
Another note that comes up is the idea that Mon Calamari ships are, by design, able to act as submersibles. I can't really argue any changes to the main stats beyond the shields, but that's just my view. Anyone have any input there?