EDIT: The command works fine - check my comment below.
Since the query-pool commands are broken (I'll create a report soon, as soon as I find some time), I have to use putWeaponPool as a workaround in my campaign.
However this old command, being there since OFP, seems to ignore the Arma 3 items.
In the editor, add a crate (I used NATO basic weapon crate) and name it crate.
Then add some weapons, magazines and ITEMS (I tried it with scopes) into the WP, using the addWeaponPool, addMagazinePool and addItemPool commands.
I tested it in a campaign environment (which is the overall goal) but the bug reproduction should work in a single mission too.
After having filled the WP, use the putWeaponPool command on the crate.
If the bug is there, only the weapons and magazines will be transferred to the crate. But NOT the items.
I'm sorry, guys... :( I noticed that I had a trigger on the mission area which removes all items from cargos...
The putWeaponPool command seems to work just fine.
SORRY!