In my campaign, I have one Navigator (PC), one Astropath and one Astropath assistant (NPCs). I think a single Astropath without a choir, or, in my case, assistant, would far too often lack the psychic strength required for communicating over the vast distances of the expanse.
Concerning Navigators, I would put no more than two on one ship: One primary navigator and maybe one apprentice. Many people state that loosing the only navigator means losing the ship, an ancient and unbelievably valuable piece of technology. That's true, but I'm not sure whether the ship is worth more than the Navigator or the other way round.
The Mechanicus will not like hearing of the ship loss, but they cannot stop the Rogue Trader from acquiring or even building another vessel. The number of available Navigators however is limited, while Navigator Houses have many clients to serve. Would they risk putting 4 navigators on a single vessel which might simply be destroyed by warp storms or aliens etc? Would they risk making 3 members of their house more or less disposable? Or would they rather provide a single navigator, so the captain is forced to protect him with every means available, while the others can serve other Rogue Traders who in turn become "vassals" of the Navigator House? Furthermore, it's not the RT's ship that earns the long term profit of the Navigator House, it's the shares in the trade routes and colonies he established for his house. These will endure the captain's death and the destruction of the ship.