You can pull the mushrooms out and compost them, because as they deteriorate they may attract flies and little beetles. They won't hurt your onions, though, and are a sign that your soil is rich with fungi, which enrich the soil. Not all species produce fruits (mushrooms) but many do. NOT edible. We use a lot of wood chips to mulch paths, and see lots of different mushrooms. They seem to like to grow under peppers, go figure.