Most likely they were ditched after returning to the mothership. The warheads are most likely not with the Chariots.
The British also used a larger midget submarine, the X-Craft.
The US Navy UDT operated Chariots for some years after World War II. They were a forerunner of today's Seal Delivery Vehicles (which are now very far advanced over WWII capability).
d.o.l.
Criminal Number 18F