Unless it's really cold outside, my chicks are moved to an outside brooder at 3 weeks. If it still gets chilly at night, I'll put a heat lamp in there too. We hatch 22 eggs every three weeks (14-20 hatch each time) like clockwork and, yes; they stink. We've used newspaper, paper towels, puppy pads, dry grass clippings, pine shavings and sand as litter; of all those, dry grass seems to be the best odor absorbing of the bunch but the chicks pick at it. We've never had one choke or suffer an obstruction but the possibility is there. It's also as cheap as raking it up after mowing.
My wife used to be heartbroken at putting the peepers out at 3 weeks but she's gotten pretty mercenary about stench abatement because the indoor brooder is in her craft room, lol.