The producers say intakes. We assume like to take either free hydrogen as fuel or maybe tachyons or something for their wave motion engines.
On the battleships, battlecruiser, and submarines they looks more like intakes with grills over the front while the older style ships seem to be open.
The production staff said they are dark when the ship is powered down, green when cruising and the more traditional orange-yellow glow when powered for combat. They suggest it is so that their enemies know when they mean to fight.
The carriers don't have noticable "eyes" on them anyplace.
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