I think I'd prefer to not be able to see them, as it makes it harder for people to get together outside the game mechanics and team up across factions or (worse still) betray their own empire for friends in another faction. I don't think it will be an extremely widespread problem, but I'm concerned that it may be a bigger issue if players can easily identify each other in the game.
That's something that could always be changed in a patch tho, so it doesn't matter too much I guess.
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