The vaults in the reef and the iron temple have your items from earth transmatted over. Think of it as an atm machine. If weapons were stored in the reef, iron temple and earth then everything you own would need to be duplicated twice from the original. So by destroying the vault in the tower means the weapons and gear are done for, they cannot be transmatted out to the reef or iron temple. Doesnt it seem odd that theres no opening in the vaults to pull out a weapon? Your ghost holds onto your gear thats not on your person and when you want to use it, he materializes it for you. Equip a weapon and then quickly aim it, youll see its still in the process of materializing. Thats exactly how youre able to respawn as well. Ghost pulls all the atoms that make up you and then materializes you in a safe spot which is somewhat the same as the theory of teleportation in real life.