My brother runs a machine shop. One customer has him drilling 3,700 holes, 0.08" diameter in a piece of plywood. He programs the machine and lets it run. The program is easy because of the simple pattern. If holes are not in a uniform pattern the programming is a bit more challenging however at some point the CAD file can be downloaded easing the programming burden.
So, if you need lots of holes drilled where spacing, intervals, etc is easy then anyone with CNC or better equipment will offer a lower cost. As complexity goes up so will programming costs. It would seem that having a proper CAD file will help to keep costs down.
My brother has another customer who requires 3,600 holes to be drilled in a 1/4" thick aluminum plate - to copy exactly the pattern in a piece of perforated metal. He works it out so a young lady who runs a landscaping business can work on it (drill press) between jobs or on rainy days. She puts in a few rather dull hours here and there over the course of a week or two and it gets done. You might consider making a metal pattern which might ease the layout/location burden.