Um...this seems obvious but...
Is it not reasonable to think that [V] might once have intended for real-time dynamic lighting to be possible, a la the ship lights that illuminate the hull of the USS Enterprise NCC-1701 and NCC-1701-A (and B!) in the Star Trek movie series?
In other words, I think they may have once intended spotlights to be possible, cast from certain parts of the ships. Take a VERY close look at the Bastion Cutscene and other FS1/FS2 cutscenes. You will notice that some of the ships have floodlights casting light beams across their surfaces. I believe those light beams are what those light points were for, and I bet you all that the SCP Team can probably be put to the task of getting those light points to function.
As it is, in the SCP, currently people are simulating lights through TEXTURES of lights, a la glowmaps and shinemaps. But those aren't REAL lights.
I bet that what [V] had on their ships were REAL lights, and its up to us to find the way to enable them and make them work.
Just a theory, anyway, I could be wrong. But I think any SCP project guys who are reading this might want to look into it.