Both are excellent against the elements, creating a layer of water-resistance & extra UV Inhibitors.
Latex is a water-based solution, and Varnish (paint) is an oil-based solution. The varnish treatment is more rugged and creates a "stiffer" net, and therefore extends the life-span beyond a Latex treated net. This could be a pro to those looking for max life-span, and a con to those who need to collapse their net into as small of a space as possible. Varnish also tends to have a stronger odor, and is not recommended to be used in closed-air spaces without ventilation.
More Barrier & Backstop Nets Frequently Asked Questions