My housemates (husband and wife) bought their 6 year old girl a mini lop rabbit. It was kept outside in a cage and I provided an old t-shirt to drape over the cage during the night. She only had it for 13 days and was quite attached to it. Unfortunately she didn't place the t-shirt over the cage when she finished playing with it the night before and come morning it had died from hypothermia (breezy and chilly during the night).
We noticed the rabbit had died at around 9am that morning. The husband had already gone to work and phoned his wife to dispose of it before their daughter woke up (around 11am) and tell her it had run away during the night. His wife chose to let her daughter see what happened and hold a burial for it.
Come 11am the girl was upset, teary eyed, and wept all morning/afternoon. We held a burial and we explained to her why the rabbit had died and how it could have been prevented. Soon they will get her another rabbit.
TLDR:
If you knew your child's pet rabbit died before they did, would you dispose of the body and tell them it ran away during the night, or, let her discover the rabbit as is (cold/stiff/eyes open/yep, it's dead)?
Tell the truth. Sooner or later kids will find out about mortality and then wonder if you lied years ago.