Lots of very interesting thoughts above, and my thanks to all.
For my part, I would slow down and look at what we do absolutely know. These are areas that either generate light (and also possibly other parts of the EM spectrum), or allow light (and other parts of the EM spectrum) to pass through from beneath. There are three. A fourth is apparently held in reserve or is seldom used.
So they could be skylights, yes (spacelights? ) but what else do we know of from canon that generates energy. Sensors and communications have been mentioned, but both seem to depend on the subspace spectrum, and I'm loathe to think that ordinary photons play a part. We also have deflectors, shields, transporters and tractor beams. Unfortunately, I don't see why any of these would need three big, glowy squares only on top of the primary hull, but all would fit in with holding a fourth "in reserve."
Or maybe the business ends of transporters, for example, are beneath the primary hull, and we're seeing the butt-ends peeking out on top? Just thinking out loud.
Maybe they're art.