My only complaint with the glows are that it's not necessary to have red on one side, and green on the other side of a ship. I can just imagine the tech comments:
"Boy, we'd love to have that Myrmidon squadron up and running to help defend against the Shivan bombers, but we're clean out of green bulbs. The last convoy carrying them got blown up in another Shivan attack. Should be in by Tuesday though."
Although I can see it being handy for certain pilots who have trouble telling left from right.

Intelligent placement seems to be the key. The ones on the Ursa look awesome, like little targeting lasers flashing on and off. But some of the others look like they're there for decoration's sake, and don't help immersiveness. Glowpoints on the Pegasus, for example, don't make much sense, even though it
does sound like something Command would do.
"Alpha 1, we've sunk millions into developing this new stealth fighter. For this mission, you're going to fly deep into Shivan territory with four sets of 800-watt strobing red, green, blue, and pink lights. Your objective for this mission is to scan the Shivan fleet without being detected or seen. Dismissed."