Lynzi, I'm sorry to hear about your son's bun. It's not uncommon to lose one unexpectedly, but to lose one like that is so shocking.
You know your son best, of course, but I have never lied to my kids about animal deaths - especially with rabbits. For years, I've had a bit of a bitter joke about them. When someone asks me what the life expectancy of a rabbit is, I usually say, "until they get tired of it." I've kept rabbits for upward of 25 years, and over the years, I've had a lot of unexplained and unexpected deaths. I would spare your son the gory details, but I think it a bit unkind to string him along, letting him think there is a chance of his rabbit coming back, when you know that it never will.
Rabbits can be astonishingly brutal to each other, causing horrendous injuries, but if there was flesh missing, that to me says "predator." It might have been a possum, or maybe a weasel. Dogs can do horrific things without even getting a rabbit out of its cage. What is even worse than what you experienced, is having an animal live through such an attack, and you then have to put it out of its misery.