Answering the original question:
Glass looks nicer, weighs more, and is easier to break. If you go glass, get two 24"x24" (ish) squares, not one 24"x48" piece. It'll be easier to handle, harder to break, and you can set one on top of the other if you only want to work on one side. Since you're rimless get some little tabs and undersize it a bit so it sits just inside the tank, at least at the front. I'm not sure what it takes to clear your overflows and plumbing in the back. Other than a nicer appearance, that way when the lids drip in goes in the tank. Other than looking a bit nicer glass lids have the benefit of being easy to clean with razor blades.
Personally on bigger tanks I tend to use polycarb (not acrylic) just because it is harder to break. It will bow visibly with a large temperature differential, but won't have the same bowing issues as acrylic.
Whatever you do, drill a 1.5" or so hole in each piece. For squares I'd drill it right in the center. For a large rectangle I'd drill it in either the same places, or 1/3 of the way from each end. This makes putting in food, pulling water for a sample, and simply handling the lids much easier. It's also a location fish are less likely to jump at, although you can always cover them if you're concerned.
As to evaporation rate, it's a function of water temperature, air temperature, and humidity. Because this is all local to the surface, you can also influence this with surface air movement (ie fans). I have a suspicion that scummed over water also evaporates slower, but that shouldn't be an issue for a well set up reef.
Give that Jeff's house temperature tend to be close to the average outside temperature I suspect the reef is often warmer than the surrounding air.
For a given humidity lever and water temperature there will be more evaporation at cooler ambient air temperatures. The air warms up as it nears the aquarium water, and then since it can carry more humidity it picks some up and then wanders off. Of course it might condense it out elsewhere when it cools back off, which is why fish stores in warm climates often have huge condensation issues in the summer.
Fun addition, if your aquarium temperature is below the dew point your aquarium will (slowly) fill instead of lose water to evaporation. Of course you'll also have a really awful condensation issue on the outside of the tank, and are probably in a very warm and muggy climate running a chiller.