I've been using polycarbonate for a number of years now and I really like it.
First it's cheap and you can get useful sizes at Home Depot.
Second it's easy to drill and cut. Don't bother with acrylic. Step drills work very well to create holes for sockets.
Third, since it comes with a protective covering on both sides you can mark out where you plan to drill, cut etc.
Fourth, I don't cut myself on sharp edges as much as I do with aluminium.
Fifth, it helps to be able to see through the top plate when you construct things. Of course this would apply to glass or acrylic as well.
Sixth, it's very strong, almost unbreakable.
The downsides are
First, provides no shielding as Paul says.
Second, tends to collect dust quickly.
Third goes either way, you are proud to show off your impeccable wiring or you are ashamed to show off your rats nest.
In your case if you are really determined to use glass, build it first with polycarbonate. If it works out well, then repeat it exactly in glass using your poly as a template.
ray