Japanese Stab Binding - in mass quantity

Setting up a jig to make the holes is about as much automation as you could hope for in this type of work. I have seen some similar bindings where the binder used a paper drill to do the holes in a large stack of copies at a time, but the holes had to be larger than needed due to that process.

You make progress with somethign like this one copy at a time. Allow plenty of time to complete the work.

Get around a drill press and a 1/16th inch drill bit, set up a wooden jig and stack a few books worth of stock up at a time, separate them on the open side with post-it-notes; if they’re pretty thin you should be able to do quite a few- but bear in mind 1/16th drill bits are kinda short.
These should be stacked with some chipboard on top. The chipboard should be cut to the same size as the books, and you should make some holes in it that are the position you want your stitching holes to be in the booklets. Line the drill press up with each hole and drill.

Then it’s just a world’s worth of hand stitching.

You might want to consider binders posts if you could bend the materials/design next time- there should be inexpensive plastic ones, though it’s not nearly as tasteful as stab binding and it’s beautiful patterning; however, the means may be suited to the end goal, whichever way it’s going to go.

I second the jig, or at least a piece of chipboard with your hole locations marked on it. For larger orders I typically punch with a 1/16 bit (or a wire size bit depending on the size of the thread or twine), and chuck it into an old hand brace. This one is similar to the one I use. http://studiohousepro.co.uk/fugitiveauthor/assets/images/ANSWER_3.jpg
I like this over an electric drill, because the lightness of it’s design makes it easier to maintain a vertical hole.

Best of luck!