I can't find how to remove items from the room when working in the items layer. Each click just adds another item.
You can simply place the white (or black) world tile on top of the item to replace it. I don’t think there’s a way to „delete“ a tile/item in a room, you can only replace it with something else.
One way to think about it is, a tile is always something rather than nothing 
When you start, they're either "black" or "white" tiles, not "empty."
(Another related point is, tiles are always one thing only—they're a world floor, OR an item, OR a wall, and so on. Two exceptions are exits (which are really logical overlays on top of the graphical tiles) and the Player (which is the last thing to get drawn in the game—this is one reason why many PulpScript functions can only be used in the player's draw event.)