I was such a deprived kid - I didn't know meat was sold in the grocery store in prepackaged saran wrapped bundles until I was in high school.
It's possible the headless deer was actually hit in the head by a car. Hence it's state of still looking like a deer. Or it could have been partially decapitated and some scavenger - dog or what have you - carried off the head.
Taking the antlers does seem like they were just being utilized. The meat probably wasn't good enough to salvage.
I know I have been late for work before due to a fresh deer hit with a vehicle in front of me and everybody gutting and dragging off the deer immediately.
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I never thought twice about it.
I think maybe the best thing for your nieces would be to actually meet some real life hunters who can explain the process to them. The more you try to shelter them and the more anxiety you have over an issue the more traumatic you actually make it for them. There is an overpopulation of deer around here, so you are going to see a bunch more road kill before it's over. Plus it's rutting season...