There's also the problem that is inherent to magnetic fields, which is that they extend to infinity with a falloff of interaction strength. This means that they can be interacted with by other strong magnetic forces. Flying near a magnetar or other strongly magnetic object with the scoop on would be bad mojo.
Magnetic force drops off nearly exponentially with distance, so this is not really much of a problem unless you're flying VERY VERY VERY close... at which point you've already messed up somewhere. Space is really, really big and really, really empty - it's not like the ship captain is suddenly going to ram into a stray magnetar like it's some kind of galactic pothole or something.
Or, to look at it another way, gravity also extends infinitely but you wouldn't consider a physical scoop to pose a special risk of sucking the ship into a black hole due to it's extra mass, would you?
No, but I wouldnt have to worry about the very large scoop accelerating iron based micrometeorites or pockets of cold plasma (Or even the nuke plasma behind the vessel!) toward the scoop, and thus toward the ship either. A magnetic scoop has its own series of hassles associated with it, and a big honking physical one stuck on the prow has its own as well.
In this case, since you are on course to a very distant (a few dozen to a few hundred light years) destination, any alteration of your course from even a slight tugging can be quite significant. Gravitational bodies would indeed present a hassle, even if they are not anywhere near strong enough to cause immediately noticable effects. It would be sufficient to throw you off course.
10ebbor10: That wont work, because you are not assuming that your reference frame is "stationary". When we measure the doppler shift of receding galaxies and stars, we are assuming that the earth's reference frame is stationary, or can be treated as stationary. However, if the vessel is moving at a significant fraction of C, then what if the star you are measuring is moving towards the ship, while you are moving toward the start? The blueshift will be higher. Unless you know the velocity and vector of the reference body, you cant use it with the doppler shift calculation to get a discrete value for velocity. There is a significant variable that you are not accounting for.