Damnit, I had a huge explanation as to my position on this subject, but this worthless board lost it and I forgot to use my usual foolproofing methods. I'm too annoyed by the whole situation to go and type it all again.
To sum up, the games have enough errors that you have no reason to trust them, they're just there becuase some programmer, artist, or designer felt they made for good gameplay.
I don't really know that much about modding FS2, so I can't be too sure what can be done. If I were to have an ideal, it would be that the shields be divided into multiple arcs, each with a separate projector component, on the surface, not obvious, and either physically destroyable or at least destroyable as a subsystem. The exception being the bridge arc, which would be housed on or near the domes. The domes would be noted primarily as sensor components, and definitely destroyable. That the shields must be downed first is the best thing I've heard all day.