Leela and the crew still scoop Nibbler's poop. It was addressed in Bender's Game at some point, though I can't remember if it was Leela or Fry who said it. (Nibbler says something like "You know I can talk? But you've been letting me use a litter box all this time!" and one of them just shrugs and tells him he's "cuter that way".) I would assume they're still incinerating his poop, even if it's not starship fuel anymore. And he does use a litterbox, as Bender dug through it looking for "buried treasure" in Bender's Game.
So there you have it, tnuk. All you ever wanted to know about Nibbler's poop in one handy post! I take my leave now.