We actually built a first-gen version of this machine out of 1/2" acrylic. It looked amazing, but the acrylic did present a few issues.
Acrylic is much heavier, harder and more brittle than masonite. This does not necessarily make for a stronger gantry; my guess is that the strongest material for this design would be a high-quality 1/4" plywood (steel or aluminum plate would be even stronger, but that calls for a different jointing method and more $$).
The weight might add some extra stability, especially to the attachment points where the gantry sits on the Y-rails. Here we use an advanced gravitational joining technique (the gantry sits on the rails, held on by its own weight).
The motors do get fairly hot--we measured them at about 130F--which could be an issue as far as bending (acrylic likes to bend when heated).
Since all the tab slots in the CAD files are 0.24", this may be an issue as not all 1/4" acrylic is actually 1/4" thick so you may then need to adjust the CAD files accordingly.