I've noticed that when you hide bodies correctly they don't vanish which gives you an idea as to if you have hidden them properly.

Now there is one point on the 360 where I dropped this one female Weeper with a sleep dart and she vanished before she even fell (and no I didn't have that ability that turns dead enemies to ash). I couldn't even get to her to stow her away and no alarms went off with people having lightning bolts coming out of their heads. It just decided "This body is going to be found" and messed up the stats.

In fact I have had a bodies vanish right after I choked them too (the first Overseer in the Back Yard area). Took me a while to figure out what was happening.