using a drill on polycarbonate requires that you alter the drill bit. You have to change the angle of attack on the drill head, to make it "scrape" instead of "dig".
It's the digging that causes the cracks and such. If you have a grinding wheel, you can grind down the leading edges on the head so that you can make perfect holes.
Depending on the size, if I am putting larger holes in, I love using spade bits. Their scraping action is perfect for this application.