Thanks to all-too-soon un-necessary respawns, nothing is very safe. I suppose the VERY simple concept of you taking over a dead man's home was too much to envision for the dev team. Or that a dungeon you cleared a week ago might remain unpopulated and un-junk-ified is just too unrealistic. it's more believable if Dwemer ruins get flooded with more ancient artifact-creatures on your behalf, or that more ancient Draugrs burst AGAIN from their final resting places that you've already seen.
Not too many containers are very "safe" thanks to stupidity.
But the two barrels outside of the smith in Whiterun stay safe for a very long time--as well as the laboratory containers in Blackreach.
Sorry if that didn't quite answer you...