1) You don't see crew on other ships primarily for client performance reasons (not just rendering them, but updating the physics data needed to make them animate properly). I'd love show them, actually, it just requires time and effort that have been devoured by more important things.
2) There was, for a time, an option called "Extreme Details" that showed crew on all ships. It was always buggy, it was always confusingly named, and it was primarily added for spectators before the spectator improvements were done. It is not likely to return.
3) There is no .ini file. The only way to change options outside the game in Windows is through the registry, which I don't really recommend. This is simply how the Unity engine stores this stuff by default, and we haven't spent the effort to make it work another way (though we'd like to).