Whether dolphins or the fictional Takaya's whales mentioned in the TNG Tech Manual in the navigation context ever went extinct is not established. All we know is that humpback whales died out.
I agree. But then, your shrimp argument is invalid.
Another thing: if we assume humpback whales are the only ones who can talk to deadly-alien-probe, the motivation for starfleet to have more of the whales seems obvious. ...already writing a novel : The Return of the Deadly Alien Probe.