The Korean airplane shot down in 1983 was flying all lights off. I feel that if they had the logo lights on the military pilot would have been able to identify them as civilian and therefore would not have fired at them, or taken more trouble to force them to land. Maybe.
I was over Kabul at night some years back, cleared to climb to FL310. As we climbed I saw a BA 747 immediately above us (had to crane my neck to keep them in sight). I stopped climb a few hundred feet below them and asked ATC if they had any traffic in our area, and was told in a rather urgent voice to immediately descend to FL290. I can't say that the logo light made it more likely that I saw them, but it might have, since the logo light is quite a good alert, and allows the airplane to be identified more easily, as well as to see its vector.
I personally don't understand the thinking of those who turn the logo light off at night, at any altitude. What are they saving? electricity? That's the justification the Korean crew was using.