Besides helping to break up the stream for better idle and allowing idle air in, the holes also serve as a vacuum break. With the vacuum pulling on the fuel without a hole there, it can suck a BUNCH more fuel into the engine. Things generally change drastically in regard to idle leakdown if you tape the holes off. Big adjustments needed.
They aren't critical in a supercharged engine...when a guy has way too big of a hat on a tiny engine, you pretty much HAVE to get rid of those holes to make it work or you'll never get the idle down.
In a naturally aspirated engine where the nozzles are in the runner, it really helps to have them - even if they're smaller than the standard 1/8" hole.
Related story: I tried getting rid of them on my car last summer to see what would happen...I was hoping for better idle control. We start and warm the car up on a bottle. Usually we get 2 minutes or so on a small bottle of methanol WITH the nozzle body holes. I put bodies in without the holes and it was literally out of fuel in about 12 seconds...it SUCKED the fuel out of the bottle instead of letting it gravity feed. I could have made the nozzles much smaller and probably made it work, but I put the bodies with holes back in and got our 2 minutes back. Also it idles much smoother and more even idle temps across the board with the holes when on the bottle.
Bottom line is, I do think they are optional but even when properly adjusted to suit either way, you might find idle quality and temps are better with them. But of course that's only at idle. At race speed, they are irrelevant for sure.
Spud