bah12, I kind of agree with you. The reason I didn't like the mom's response was because it seemed so dismissive of the entire incident--"Oh, it wasn't you playing a prank on the kids? Must have been a ghost! Ha ha!" She didn't seem to take it seriously.
Now, of course I don't know the mom and the whole backstory like the OP does; but if the mom heard the story "in triplicate," maybe she drew the conclusion from the stories that it was the OP's son who did it, or the OP herself, or just the dog, or whatever. It's not like the 11-year-old is going to say something to implicate himself to his mom. Though the OP feels almost certain it was nephew who did it, and the evidence she presents makes it seem likely to me, too, she doesn't feel it's solid enough to actually accuse the boy--there's a reasonable doubt, in other words, and for exSIL, who wasn't there and probably hasn't heard the timeline the OP gave us, it probably seems even more up in the air. So, just based on this--and again, I understand that knowing them personally could change things--it doesn't seem weird to me that the mom doesn't automatically think it's one of her own kids.
That's why I think the OP should make it clear to all that there will be consequences for this act; or at the very least, that there will be consequences if it happens again. Maybe that would make exSIL take it more seriously. I guess exSIL doesn't really need to take it seriously, though, as long as the OP holds her ground about the consequences, so maybe that's a moot point.