There is logic to what Russ says, i.e. alternator continuing to power the motor, pumps etc etc..
However, many electrically operated isolators (solid state or relay) also make/break the charging connection from the alternator to the battery, so they well and truly isolate them.
Re which wire to break, +v or -ve? well if the 'break' is right next to the battery you could argue that it makes little difference BUT if the isolation point is further away, then breaking the +ve will leave a large cable to the break point that could short to ANY earth point along its length in the case of an accident/impact.
If you break the negative, the section of negative cable from the battery to the break point would only be a problem IF is shorted specifically to another +ve cable and it should be possible to prevent this with careful placement of cabling.
So for my mind, breaking the earth (-ve) is safer...
One thing with these systems, always remember that they will make wiring for alarm and electric central locking systems more complicated esp if the earthing circuits are broken. So if yours is a road car as well as track, consider the requirements carefully...