Why not just put the dots on a separate layer and tell the printer?
That should be possible.
Draw the perforation lines as ordinary stroked, unfilled paths on a separate layer . There is no need for them to be dots. A printing house is going to use either an on-press perforation "tape" or (better) a separate operation on a different machine. The hole size and frequency are going to be functions of the printing house's hardware, not anything you build into the file. Your purpose in drawing them on the page is just to indicate location.
Name the layer PERFORATIONS. Be sure to inform the printer you have done this. (There is no industry-standard procedure for communicating perfs, scores, folds, die-cuts in a file. So clear communication with the printing house is paramount.)
What James said.
I would, additionally, be prepared to provide separate files (Illustrator documents) for things like perfs and die cuts, depending on the capabilities and requirements of the printer. You should use clear, unambiguous file names, and, of course, your registrations must be precise.
When I send PDF artwork, I duplicate my native file, delete all, place the perforation line, and send it as a second PDF. Do any of you have a more intelligent or efficient way?