As per a recent conversation with the owner of the factory that makes at least the RV-4 and RV-8 canopies:
Use a standard #40 for 40 holes, diamond cut plexiglass bits for holes up to 3/16 and step drill bits for holes larger than that. Go slow at first, speed up as you go and slow down as you exit the material out the back. Back up with wood. This comes from someone who does it every single day.