I would post this in the "General Material Machining Solutions" section. I think you will get better responses in that area.
Also IDK about EDM machines but I am surprized no one has meantioned a EDM machine.
Are you trying to drill the lenth of the bolt,, or just through the side of the head for adding a saftywire? It almost seems it would cheaper to buy the bolts with the hole already in them, or maybe your trying to find a way to just do it cheaper than buying them?
Also I have a feeling there may be more to this than meets the eye. Could drilling this hole effect the strenth of the bolt, could they need additional treatment after such a machining op?
Jess
GOD Bless, and prayers for all.