The government tried to compel Apple this way (not through a subpoena but an ancient law called the All Writs Act) in the San Bernardino shooting case but they

The government tried to compel Apple this way (not through a subpoena but an ancient law called the All Writs Act) in the San Bernardino shooting case but they were able to unlock the phone through other means so the case just ended up going away. It probably depends on whether Whatsapp can argue it's unreasonable, the government has other investigative techniques available, etc.