Yup, i think it doesnt matter what color do you use on your ship, its replaced by the shield effect you are wearing. Anyways, the "color" of the ship cant be changed, only the color of the hull pattern as far as i know..
You can turn off the visuals of "special" shield types, like the Jem hadar and Breen shields. Click on the shield icon on the ship character window and select "Disable Visuals."
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