(post edit) TLDR:
If you Upgrade to the 4x4 Cargo Platform, you will lose any items or modules such as crate stampers and air cyclers stored at the bottom of the Crew Quarters, if you have that room installed.
So I've encountered a sort-of softlock (for taking shipping jobs at least).
I placed the crate stamper in a small corner of the crew bay (I think that's what it's called). It's the room that gets placed just above the room with the cargo platform. The stamper was placed in the lower-left corner of that room.
The room was packed to the brim with miscellaneous goods.
On the way to a place I was going to drop off some waste barrels I was going to pass by a planet with a shipyard and I had a pair of upgrade modules with me, so I decided to take a stop and get an upgrade, notably, to the delivery platform.
SO.
I purchased the upgrade and returned to my ship where I found that all of the goods in the upper room had shifted down a space and my label stamper disappeared.
I was hoping that taking a shipping job from the company would give me another stamper. It did not, and now I can no longer take shipping jobs because I can no longer stamp the shipping containers.
The ability to purchase new stampers would be appreciated in the case of little mishaps like this.
Otherwise, I've been enjoying the game immensely and can't wait to see what comes next!
EDIT:
The compactness of cargo is not a relevant factor as I have just discovered.
I started a new file and lost 2 air cyclers to the exact same bug.