Taken from Wikipedia:
There are actually
three Stanley Cups: the original bowl of the "Dominion Hockey Challenge Cup", the authenticated "Presentation Cup", and the "Replica Cup" on display at the
Hockey Hall of Fame.
To flesh this out a bit more:
The original bowl which sits in the Hockey Hall of Fame was used from 1892-1963. It was originally just a bowl, then was attached to various bases over time. It sits in a vault (literally, a de-commissioned bank vault with heavy door) inside the Hall of Fame where it can be viewed, but rarely if ever makes public appearances elsewhere.
The "Presentation Cup" is what we all think of as the Stanley Cup. It's a replica of the original bowl, which sits on the big barrel-shaped based and gets awarded and then passed around among the players. It has been "the Cup" for the past 55 years.
The "Replica Cup" is simply a body double, because they still need to have something on display at the Hall of Fame when the Presentation Cup is traveling. The Replica Cup is for all intents and purposes just a decoy for the fans.
It honestly wouldn't surprise me if the Presentation Cup has a GPS chip as suggested in the OP. It is the only one of the three which is regularly exposed to the possibility of theft, which is why they hire handlers to travel with it. It would make sense if there were a secret Plan B in case it ever gets away from the handlers.