A slightly modified #1 could work too - I like red highlights, but it seems a bit fiddly on that model and I'm not sure how well it would look at a distance.
I understand that overall №2 - the basic one - is the best, so I'll put it into the game. However, some of you (and me too [embarrass]) like red coloured picture, because it makes ship look more aggresive. I'll try to add some red elements in more refined manner, but just not sure about the outcome.
2, There is no point in making a ship stand out, especially if it is supposed to not get blown up immediately. Sedate colors are logical, and when the thing appears out of nowhere (because nobody noticed it earlier), it would be very intimidating.