I've experienced something similar to this in my Realm on the Xbox. I had a farm full of animals I bred, left the chunk and loaded up a zombie farm for XP, after some time (can't say how long), I noticed more and more animals disappearing, first pigs, then sheep, llamas and horses, but oddly enough not cows. Also found chickens escaping an automated chicken cooker, come home to a room full of chickens. My villager breeder lost all of the villagers it bred. I've resorted to curing zombie villagers and keeping them in boats for the time being.
I can get it to lag with just one named shulker box filled with named and non named items.
I can also confirm this problem still exists on Xbox One. The Guardian Farm we created in our Realm spawns no Guardians at all. I switched the game to Peaceful, logged in, logged out, switched it back to our normal difficulty and 1 Guardian fell through the trap. One.
I still experience this problem on Xbox One in my Realm.
Tested it with the silverfish in carts and boats, no suffocation.