I am assuming the “sky lights” you are referring to are the plastic panel roofing types that are used with steel roofing panels? Not the type use in a house that is basically a casement window designed to be installed in the roof.
If so just use spray paint that is meant to be used on plastic. Make sure the surface is cleaned really well before spraying. The product might suggest what it the best “primer” cleaner to use so as to get really good adhesion and not peal bubble over the course of time. Or ask the paint salesmen what is the best product to use.
Just guessing but if I was going to do this I would paint the inside. The outer surface is exposed to the elements and subjected to much more “wear and tear” and become a maintenance issue.
Unless there are a lot of these installed I think you might be disappointed in the results. It’s not the “light” coming through that’s heating the “air” its the surface that the light is shining on and heating that up. This is called a heat sink which heats up and radiates.
In a passive solar cabin I lived in we would put down a white, lite colored rug in the summer to reflect the light, solar gain effect. Or just closed the blinds when away. The roof overhand around the house was designed to extend far enough out to so that the high summer sun didn’t shine directly into the interior during the hottest times of the day. The winter sun “hangs” lower in the sky. shinning directly in the windows through out the day heating up the interior nicely.
But the roof of any structure acts the same way. Its a giant heat sink and acts like a convection oven on the interior. Heated air rises but if it has no way to exit the roof peak it just keeps expanding filling the interior with hot air exiting through the open areas at the surface level.
This is especially true with low pitched roofs which most barns are built with these days. 8-12, 6-12 roofing trusses are the most common pre-made and cost effect. To get the most “sun concentration” on solar panels they have to be set at idea angles to the sun. Which is between 26 to 33 degrees. The same angle that an 6-12, 8-12 roof pitch gives. Making it the perfect “heat sink”. Especially if the broad side of the roof in exposed to the south, south west.
That being said without the benefit of seeing how the barn is constructed and going off the descriptionit doesn’t sound like it has a high peak, ridge line and loft. IMO this is the problem not the sky lights.
Installing a ridge fan, antic fan should give a pretty good bang for the buck as long as it is sized properly.
If there are a lot of sky-light panels to be replace this is not going to be inexpensive to have done. IMO based on descriptions given you will get much more satisfaction spending the money on a properly sized cupola as others have suggested. Sizing is key. The size be it for a fan or a cupola is based on the amount/volume of air that needs to be exchanged. People make the mistake of not doing the “math” and waste money installing something that is way undersized to do the job. Especially cupola’s. They end up with something that looks nice but is not really functional.
But in the end depending on location and summer climate the barn is going to get hot regardless. Ours is a giant bank barn. The top of the roof is around 50’ from the ground. The stable area stays reasonably cool for quite a while into the summer. But by mid summer we still have to use big barrel fans in the isle way when working and stall fans.