I like the idea of the flat top, but have a couple of potential concerns.
The first being that even LEDs listed as waterproof don't always work out to be so, I've had a few LEDs fail because of water ingress. To be fair though, it's mainly been in marine systems, so it could be the salt helping to penetrate the LEDs.
The other concern would be reducing the air gap in the top of the aquarium, which could affect the gas exchange in the tank.
As for material, I wouldn't use acrylic, it has a tendency to bow. I'm not sure if it's the heat or moisture, but it likes to curl up at the ends. I currently have a 10mm thick piece of acrylic on a 50l / 60cm tank, and find I have to turn it upside down once a month to straighten the bow.
Have you considered using some 2 or 3mm thick aluminium sheet? You could paint the outside black to match the tank and keep the inside naked aluminium; this will aid the LEDs as a heat sink and the silver colour will act as a reflector.