I've been using a shulker box loading system and noticed that some of my shulker box's have gone missing.  I've done quite a bit of testing, and it seems that when a piston breaks a shulker box the shulker box will bounce through various different blocks.

In my setup I have a shulker box in the middle, behind the box, feeding into it is a hopper with several hoppers on top of this feeding into said hopper.  Directly below the box is a half slap, and under the half slab is another hopper that is to pick up the shulker box when it is broken.  On top of the shulker box is an observer that is attached to a sticky piston which will push the observer down effectively breaking the box.  In front of the box is a dispenser which has other shulker box's in it that will dispense a new shulker box.

There are blocks all around the box, so the only place for it to go is truly straight down, where it should be picked up by the hopper below.  However after doing alot of testing the box ends up sometimes in the sides of the hoppers feeding into the shulker box, sometimes on the side of the hopper below, and sometimes on the very top of the whole system.

These things are limited and very valuable to have despawn in our worlds.  I'm not entirely sure to lable this as an issue with the shulker box, as it seems to me that this is an issue with hoppers or game physics.

P.S.  It doesn't always happen, 1 out of 10 will glitch.