Luddite reply.
1000 tiny holes? No big deal. Recent project involved fabricating an air bubbler with fairly accurate hole size and spacing. 6” long piece of 3/4” Sch40 pipe, with rows of #60 holes spaced 3mm apart, located every 20 degrees around the pipe. Made a mandrel to hold the pipe in a 5C spin indexer, lined it up on the mill and drilled holes. Broke two drill bits and a couple of holes were a tiny bit out of line. Took maybe an hour to complete. No electronics involved.
As for the vacuum idea, assuming this is being done by CNC, there’s no need to completely pierce the work pieces. Even my crappy 3018 CNC router can locate Z-axis within a couple of thou. Just machine most of the way through, leaving a few thou intact. Trim with an Exacto knife and a deburring tool. Like trimming the flash on a plastic model kit.