You can do this with a hole saw, pocket knife, exacto knife, or whatever. It can be tricky or even dangerous, so be careful not to cut or otherwise injure yourself. There are air tubing splicers that are normally used to lengthen air tubing. Select a drill bit that will result in a press fit if you were to push the splicer into a hole, and drill a hole into the soda bottle cap. Before you push or force the splicer securely into this hole, make a slight notch around the base of one side of the splicer to help hold it in the bottle cap.
Thermal glue is also sometimes effective.
To use, put the cap with the splicer on the bottle, attach an air source, and with the bottle upside down, do your normal 1.025 salt water thing, adjusting the air flow so the bubbles are not too vigorous. A light source close to the bottle increases the hatch yield, but be careful you do not melt the bottle. This bottle may be hung or you can make a stand for it. I have seen them with a simple hole cut into the side and hung on a nail, some have been in stands, and others had small holes in opposite sides and the hook part of a coat hanger used to form a hanger to hang them on a line. To harvest the baby brine shrimp, remove the air tubing from the source, keeping the end of the tubing higher than the brine water in the hatchery and let the newly hatched baby brine shrimp settle to the bottom.