Not sure what height you are working with but a drill press could work quite nicely...If you have a template setup out of plastic, paper, whatever, you should easily be able to knock out 50 units in an hour. Depending on how you drill and the bit you use, you can have a clean shot for each hole. In the US here...I picked up a drill press with a 1/2" > 7" depth at northern tool for $93 a year ago. Works quite well and can drill all kinds of sideways and what not. Also comes with a foot pedal so you can vary the speed depending on material.
Example app...I use it mainly for through hole applications. I can drill a 400-500 hole board in about 3 minutes or so. Just my two cents on a possible proper tool to get the job done. Oh, don't know if it helps but I have used PCB software, CAD, and Microsoft Visio to make printout templates. That may help or may not.
Another possibility if you have a Dremel laying around...they offer an option called a plunge router attachment (P/N# 335-01). The depth sucks, but may work on your application.