Hmm... I'm looking at a Donkey Kong panel photo, and it may be relevant:

The panel is clearly wood, as evidenced by the button holes, but the joystick is right u against the veray, implying that it's installed through the top of the panel! On the other hand, that's not the original CP overlay, so the whole CP may not be original....
Heres what I'd like to know. I seem to remember the Nintendo cabinets (DK,DK Junior popeye style ect..) had a polycarbonate or acrylic sheet over the cp so I never could figure out wether those cabs had a metal or wood control panel.
Here's what
http://home.nc.rr.com/ellis1701/davesarcade/donkeykong/renovation/dkrenovation.html has to say on the subject:
"Unfortunately, DK3 used a metal control panel with the CPO glued to the surface. Donkey Kong used a wood CP with a Plexiglas overlay bolted onto it."
So we have a bit more info, but no definitive answer.