All the containers are safe in the Hearthfire houses. It is possible to get a glitch when you change the small house to an entryway which gives you a set of invisible duplicate sacks, but still all the doubles are safe as well, you just might have to run the curser over them a few times to get the right sack. I doubt anyone is going to be using all those sacks anyway.
I think it is better to just place the stuff yourself, rather than have no say in how it is arranged.
except the physics engine prevent this except the simplest case (single item taking up a whole table)
I'm pretty sure he implied, like I did, that it would be fun to REALLY place stuff on those sheves
The maximum pile of books I can create without physics or the housecarl wrecking it is 4 books, when I'm lucky
That's a massive - Doh ! Not so massive - EIGHT BOOKS PER SHELF for large wide shelves
If the shelves are two thin, the books fall
For other objects like ingredients, it's even worst, you're lucky to place 2-3 on the shelf of a large bookshelf
some tiny items like garlic are a bit easier
boots are a total pain, they show up on their side and won't stay up (even metal boots)
for me, my 'decoration' been limited mostly to piles of books because of those issues,
or the occasional single weapon on a table
In morrowind, before 'physics' got invented (a physic that don't respect the laws of physics)
I could easilly place 10 weapons on a large table, or a whole suit of armor (the armor + pauldron+ helm+ gloves+ boots, +greaves + shield),
or more if I pilled them up in a nice stack
I could create any amount of artistic display in seconds using bowls and ingredients
I would really love to do that in Skyrim,
but my success have been really limited
combining dishes + meal parts is pretty hard and tend to go 'physic' and fall on the floor
example: try to setup a plate with almon steak, baked potatoes, grilled leaks, and a tomato
and it will most likely fall to the flour
now try to set dishes for the whole family, and you're in for a laught and a massive cleanup
except it's not funny at all

- more frustrating than anything else
right now I gave up, except for books, because I know a recipe that work flawlessly - but it look boring
I heard hearthfire respawn stuff every 10 days,
is that true, and are some areas immune ?
after hearthfire messed my city houses, I gave up continuing my old favorite character
(hay is showing up everywhere in honeyside, as if the house was confused,
and both furnished and unfurnished at the same time,
showing up the junk that's there when you buy the house without furnishing)
(except of course my house in honeyside is fully furnished,
so there is that diagonal bookshelves that crashed on my table in the enchanting area)
In hearthfire for that character, I was lucky, not too many glitches
only one of the manikin with his feet in cement
(he sort of melted his feet inside the base where he should be standing)
except of course I'm restarting from scratch now
I also heard you can't have a kitchen for the kid's house because the wife want an armory