Hiyas!
Excuse my density & unimaginative nature but I cannot fathom any time or place when/where a Rogue Trader would endanger his/her invaluable Navigator in any way... So what's stopping the RT from banning the Navigator to ever set foot outside the ship? It's too GE-**** risky!
L
That's the beauty of it. When I start my 40k games I always tell the players that this is MY interpretation of 40k and I'll be sure to tell them of any major canonical changes well in advance. So if your group doesn't have a Navigator, by all means tell them that the NPC Navigator never steps off the ship. If, on the other hand, your group does have a PC Navigator then you can use any of the above excuses that I and the others have given to explain why he's allowed off the ship, or make up your own!