A loaded weapon within your inventory attempts to act like an ammo clip for an unloaded weapon in your hands. In other words, if you have a loaded Longhorn in your inventory, and are carrying an unloaded Longhorn in your hands - the game assumes that the loaded Longhorn in your inventory is a clip, therefore constantly prompting you to reload the unloaded Longhorn that is within your hands.
Pressing the 'reload' prompt, though, does nothing.