Well unfortunately there are no standard tables of limits and fits for polymers so it is still a suck it and see pastime. I suspect it will always be that way generally because of the millions of different plastics with subtle, unknown changes in the chemical make up that affect shrinkage and other properties.

Depending on your slicer a hole will be one extruded thickness small and whatever the plastic it will have a known average shrinkage rate, after that it really is suck it and see. If you are using ABS then Acetone will allow the holes to fill after it has been assembled.