To be honest, imho most of the ships and so on in the game do not look the least bit military. Most of them look more civilian than anything else, gun turrets not-withstanding. The small craft look like refugees from a WW I flying circus.
The Shivan, Ancients, and Vasudan schemes can be excused a bit due to the "alien-ness" of the cultures they came from, but there are very few militaries on Earth (if any) that have the type of diversity in appearance as represented by GTA vessels.
The Fenris/Leviathan come close to a military appearance...for a surface navel vessel at least. Even with those though there are too many open, unplated areas for any warship expected to accept enemy fire in battle, to say nothing of protection from collision with debris.
As far as windows go, each one constitutes a weaker area in the hull structure than the surrounding armour, and when lit, a nice little area for enemy gunners to target in the darkness. Same obviously goes for lights in general, at least for the targetting aspect.
That said, the Freespace textures look to have been created by "artsy" people as opposed to anyone with military experience. It's a pretty well established fact that pretty outsells drab in most consumer markets - sci-fi video games are no exception.
Hmm, I do have to wonder what the game would look like if a more military feel were used in the theme of its ship designs. Might not be bad at all - the missions themselves have a good US Navy style of play to them, though the ships seem a bit less specialized than current practice. Might fit in very well though.
