Here's my guess:
1) She does genuinely believe in ghosts
2) Her kids know this, and possibly have pulled little pranks like this before at her house (which their mom swallows hook, line, and sinker)
3) Ghosts have been on their brains lately, so the topic naturally came up when the kids were at your house for the sleepover
4) Your DS cobbled together bits and pieces of what he heard, added it to what he already knew about ghosts, and that plus the knowledge that his aunt really thinks they're real (because at that age, if a grownup says something is true it must be true!) got him worried about ghosts
5) One or more of the kids (but probably the nephew) decided to play some ghost-related "pranks" around the house. The dog food in the cheesecake sounds particularly like something a kid might do and think would be hilarious.
I'd suggest you ask your own kids (particularly your son) if they had been talking about ghosts at all, and if so, what? That might help your DS get over his fear if you can set him straight, and might give you some more answers.