Good idea, thanks! I use a lot of plastic containers for propagation, too.

I find the easiest way to make holes in plastic without cracking the container is to use heat. I usually use a metal kebab skewer, heated on the stove, but an old soldering iron (or maybe a glue gun?) also works fine. If you're poking holes through a whole stack of containers, you may need to be quick about separating them before the melted plastic has a chance to fuse the containers together.