Both approaches have their merits. If I am recording say a stereo synth I would definitely use a stereo track. It is just easier in the long run in terms of processing etc.
As for acoustic guitar say if the two microphones are in a very stereo configuration eg co-incident or near coincident then the stereo track is probably a better idea as well.
If I was micing a guitar amp though with say a condenser mic and a Shure SM57 then I would go the two mono tracks because that is not really a stereo recording. It is more recording two mono sources at once. Even with acoustic guitar if I was recording one mic in front and the other say behind the player looking over the shoulder I would also treat that is recording two mono sources at once.
That way you will have excellent control over each track eg with processing on each etc. You will also have a lot of control over the pan position of the two mono sources as well.