Swap cheat you could use for Dismantling Armor or Weapon items does not support Ship items.  The following steps will do the trick:
 - Enable "Inventory: Editor" and tick "Ship Cosmetics"
 - In ACOD Open Ship menu and select item you would like to delete
 - CE table will get updated with values
 - Navigate to pItemNameOverride->Value and copy it's value to buffer
 - Navigate to pItem->Value, paste copied value
 - IMPORTANT.  Select another Ship item
      if you are deleting Crew Theme, select another Crew Theme
      if you are deleting Ship Design, select another Ship Design
- Exit Inventory
- Quicksave game / F5, wait for Save icon to spin and disappear
- Quickload game / F9
- Done