It's the vacuum part of what is called the 'Positive Crankcase Ventilation System' and it does pass a small amount of air that will help supply adequate air quantity to maintain the correct idle speed.
The JP4 crankcase doesn't breathe in quite the same way as the J4 and doesn't have that pipe so it would be better to introduce a small amount of air via the pipe that you have to get a stable idle. However, leaving it completely open is probably going to be too much air, so make a bush to fit inside it. Make the bush out of brass or Ally so it's easy to drill. Start with a centre hole about 1.5mm diameter and increase it in 0.5mm steps until it idles properly.