Nah, the yellow is fine. I suppose options for AT could be to use a crackle effect, although it'd be lost at the 128x128 portrait size. Another option is to slightly greenify the yellow, which would look fine too.
It's going to be a nice set, can't wait until it's done.
On the smallest ship ?escort?, I would bring forward the yellow of the nacelle a bit so part of it shows more clearly. I like the set, nothing wrong with flashlights, in my opionion