I think the implication is just that Whatsapp has to hand over encrypted messages ...

I'd imagine if the police are then in control of the target mobile they can decrypt those messages.

Tbh, if my understanding is correct, I'm not sure I see any problem there. It's targeted at specific individuals for good reason (presumably following a warrant process) and requires both the messages (from Whatsapp) and they keys (from the individual's device). What's the problem?