I love everything you've done so far! Thanks for posting so many pictures - it's so nice to be able to see what other people are coming up with for their coops.
How big is your cupola going to be? I wish we could do one on our coop, but it's going to have a slanted shed roof instead.
I know it'd be twice the work, but have you considered 2 small dormers, so you get light from both directions and cross ventilation? If you do skylights, would they be able to open, or are you just wanting them for more light?
I'd vote for dormer, personally, as long as it's not too big and doesn't make the roof look off-balance with the cupola.