I followed the development of the R2 1/350 Enterprise
on Hobbytalk as well as received updates on the kit's progress (prior to release) because I was one of the 1701 Club members to get a Premire version of the kit. Gary Kerr, who researched the TOS E
for the model (and is now working on the Galileo
shuttlecraft kit) mentioned that there had been some talk of adding a light effect to the inboard sides of the nacelles, but it was deemed to expensive to go back and rework the 11 footer so the idea was dropped. It doesn't look like they were hellbent on doing it, but for the sake of completion R2 decided to include the option for lit nacelles for those who might like to explore the "what if" option. I don't recall a specific colour being mentioned so it really is up to the individual modeller.
Many years ago I played with the idea in Photoshop and did some images with blue or cyan lit nacelles along the inboard trenches. To me it just never looked right, but then I could easily be conditioned to seeing it the way it has always been onscreen.