Personally I think it a good idea, despite the trouble to give the ships a shield mesh. This could come in useful for future missions and campaigns, but to stay true to the homeworld storyline the shields could always be turned off in the main campaign that is planned.
Besides, being totally true to homeworld is good, but one must bare in mind that the game isn't always balanced the same as the storyline. Take for example the Turanic Raiders 'Lord' class carrier. It is said to be only half the size of a Taidan Heavy Cruiser, and yet in the game it is roughly the same size.
Things shouldn't always be taken as face value. Besides, like I have already said, the addition of shields or extra weaponary (not to much though) could be used in future projects/missions.
PS, to the Apoc project guys. Story I've been gone so long, life has unfortunately been taking its tolls again but I'm back now. Whats the present situe regarding sounds and music?