Tiny breather holes in bulkheads will never let in enough water to be a problem. In a capsize and flood situation, the worst you will get is a few drops. I can't say that I've ever seen any evidence of water coming through the breathers in my boats at all, despite getting lots of water in the cockpit during rolling and rescue practice.

As for making the holes, the way I do it is to drill a hole large enough to accept a piece of the red plastic tubing that comes with most spray lubes and cleaners. The hole in the tubing is very small, but the slighly larger hole in the bulkhead is easier to drill. If your bulkheads are wood, drill an oversize hole, fill it with epoxy, then re-drill the breather after it cures.

BTW, I position the holes ~1" above the center of the bulkhead, which is aproximately where the center of buoyancy is. That way, no matter what the orientation of the boat is, the breather is not likely to be submerged.