Selling the unneeded items would normally be the case, yeah, however there's numerous reasons why the player may choose to keep such items anyway. For instance, they could be manufacturing materials, or items that can later be upgraded, or they're shared as craft armaments, or don't have/can't produce ammo yet, or the player is keeping an item sample for a later research, etc.
On the craft equipment list screen, the marked items always appear, the only thing that changes is their color. Unmarking them would be the same as marking them, for instance, with a right click.
In the inventory screen, the hidden items don't appear on the Ground. As for already loaded items... it would probably be simplest if, upon hiding, they're unloaded from the craft and removed from any saved soldier inventories. My personal use case is, if I mark an item as hidden, it means I don't intend to use it in battles.
The two exceptions I can think of are:
- base defense, where all the base items should appear on the Ground, even hidden ones.
- right before an assault landing, where the player is offered all the items they brought with them on the craft (in case some items were hidden after the craft took off)
