Someone who is an aerodynamicist/Mike Burrows/all round clever git will be along soon to put everyone right but here goes.
Anything that reduces the drag (vortex behind the riders back) and allows the bike to exit the air with less turbulence is going to do some good.
Generally avoid a tailbox that is longer than the rear wheel, it could act like a sail in a crosswind. Remember a tailbox will hold less than a pair of good panniers, will also prevent the fitting of same and puts the weight higher on the back of the bike. A tailbox will make you pack sparingly and prevent you carrying tons of crap you don't need. A tailbox is a great place to mount rear lights and reflectors, batteries for Smart type lamps and even a stereo if you are so inclined.
By all means make one from ply but I think you would be better off making a traditional buck for fibreglass, taking a mould from it and using epoxy and bi-directional glassfibre cloth to produce the actual part.
Two reasons 1. It means that you can make another if you end up trashing it.
2. It will be somewhat lighter as the made from ply option needs to be effectively waterproofed which means coating it in GRP.
luv'n'stuff
J