I just read about that, and that giving them a trim can encourage better root growth and larger bulbs. I've only looked at a couple of sites so far. Okay, I just read a site that says trim them while still in a flat.
http://www.gardenandflowers.com/how_...on-plants.html Trim onion seedling stems with scissors when they are growing indoors. Gently grasp the stems and cut all the way across so that this plant part only measures 3 to 4 inches high. Trimming allows the stems to increase their hardiness so that they are better prepared when transplanted outside. Continue to maintain this height only while the onions are indoors during the typical February to May time frame.