Should the hole in polymer clay beads be made before or after baking?
Much simpler if you do it before.

You will always deal with some shrinkage with polymer clay, so just make sure that the hole is a bit larger than you will need it.  If you are really worried, try a couple of samples and measure how much they will shrink.  But it is fairly minimal, so unless you need an exact fit, it is nothing that major.