That would essentially mean more machines, so you are not reducing the (cap expense)/(time per unit) equation. Additionally electron beam optics are magnets, so driving multiple beams in the same space would be complex.
Furthermore, I had in mind that you'd have synchronisation between the beams. Consider the use case of one e-beam per chip. As each wafer has multiple chips you would still have plenty of room for parallel beams working at any one time.
As for cost, do you have a ballpark figure for how much the devices cost?