How to choose hole sizes when building a sorting sieve?
I have no idea how to choose your hole sizes, it sounds like you have thought it through, and I am sure some trial and error will be involved.  I can only suggest tools to make the holes.  

In the smaller sizes, drill bits graduated in 1/32" or even 1/64" increments are readily available.  No need for super quality drill bits if you're just drilling plastic.  

For larger sizes, there are adjustable drill bits 



These have been around a long long time, and they work very well.  Just look carefully when you're shopping for the right shank.  A lot will have the shank made for old fashioned bit and brace, which won't work well in a regular modern three jaw chuck.  

 

There are step bits that will drill holes of many sizes, you just have to pay close attention to stop at the right step:  



There are also bits I have seen sold as "stepless bits" which will cut holes of any size, but to drill many holes of the same size quickly you'd need a drill press set to stop at the same depth on each hole.  They also make a slightly tapered hole, which you may find is a problem, or who knows, may turn out tobe an advantage.  It might be better drilling from the bottom rather than the top with stepless bits.